Psyllid ID: psy17504

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190------
Protein Sequence
MGISSSELVMRARDLVFHLHCFTCISCGILLTKGDLFGMRDEMIYCRPHYEILRHRDYCGSAEIEQPMSPRPAPWQPTTVQKGRPRKRKLSVDSPTPPSEDINANVMRIPSTTLEMLHSGDLSSSMESLSYESGAGNSSPGSGVHSHQRTKRMRTSFKHHQLRTMKSYFNINQNPDAKDLKQLAQKTGLSKRVLQN
Secondary Structure (PSIPRED)
cccccccEEEEEccccEEcccccccccccccccccEEEEEccEEEcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHcccccccHHHHHHHHHHHccccccccc
Secondary Structure Prediction (SSPRO)
ccccHHHHHHHHHccEEEEccEEEHHHccccccccEEEEEcccEEEHHHHHHHHccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHccccccccccccccccccccccccccccccHHHHHHHHHHHHccccccHHHHHHHHHHHccccHEEcc
Coil and Loop (DISEMBL)
MGISSSELVMRARDLVFHLHCFTciscgilltkgdlfgmrdemiycrphyeilrhrdycgsaeieqpmsprpapwqpttvqkgrprkrklsvdsptppsedinanvmripsttlemlhsgdlsssmeslsyesgagnsspgsgvhshqrtkRMRTSFKHHQLRTMKSYFninqnpdakdLKQLAQktglskrvlqn
Flexible Loop (DISEMBL)
MGISSSELVMRARDLVFHLHCFTCISCGILLTKGDLFGMRDEMIYCRPHYEILRHRDYCGSAEieqpmsprpapwqpttvqkgrprkrklsvdsptppsedinanvMRIPSTTLEMLHSGDLSSSMESLSYESGagnsspgsgvhshqRTKRMRTSFKHHQLRTMKSYFNINQNPDAKDLKqlaqktglskrvlqn
Low Complexity Region (SEG)
MGISSSELVMRARDLVFHLHCFTCISCGILLTKGDLFGMRDEMIYCRPHYEILRHRDYCGSAEIEQPMSPRPAPWQPTTVQKGRPRKRKLSVDSPTPPSEDINANVMRIPSTTLEMLHsgdlsssmeslsyesgAGNSSPGSGVHSHQRTKRMRTSFKHHQLRTMKSYFNINQNPDAKDLKQLAQKTGLSKRVLQN
Disordered region (IsUnstruct)
********VMRARDLVFHLHCFTCISCGILLTKGDLFGMRDEMIYCRPHYEILRHRDYCGS***************************************************************************************************************************************
Disordered Region (DISOPRED)
MGISSSELVMRARDLVFHLHCFTCISCGILLTKGDLFGMRDEMIYCRPHYEILRHRDYCGSAEIEQPMSPRPAPWQPTTVQKGRPRKRKLSVDSPTPPSEDINANVMRIPSTTLEMLHSGDL*******************************************************KDLKQLAQKTGLSKRVL**
Disordered Region (DISEMBL)
MGISSSELVMRARDLVFHLHCFTCISCGILLTKGDLFGMRDEMIYCRPHYEILRHRDYCGSAEIEQPMSPRPA*************************SEDINANVMRIPSTTLEMLHS************************************SFKHHQLRTMKSYFNINQNPDAKDLKQLAQKT*********
Disordered Region (DISPRO)
MGISSSELVMRARDLVFHLHCFTCISCGILLTKGDLFGMRDEMIYCRPHYEILRHR************************************************************************************************MRTSFKHHQLRTMKSYFNINQNPDAKDLKQLAQKTGLSKRVL**
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MGISSSELVMRARDLVFHLHCFTCISCGILLTKGDLFGMRDEMIYCRPHYEILRHRDYCGSAEIEQPMSPRPAPWQPTTVQKGRPRKRKLSVDSPTPPSEDINANVMRIPSTTLEMLHSGDLSSSMESLSYESGAGNSSPGSGVHSHQRTKRMRTSFKHHQLRTMKSYFNINQNPDAKDLKQLAQKTGLSKRVLQN
Positional Conservation
no confident homologs detected

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Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

ID	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query	196	2.2.26 [Sep-21-2011]
Q9Z0S2	406	LIM/homeobox protein Lhx2	yes	N/A	0.846	0.408	0.475	1e-41
P50458	406	LIM/homeobox protein Lhx2	yes	N/A	0.867	0.418	0.470	2e-41
P36198	426	LIM/homeobox protein Lhx2	no	N/A	0.867	0.399	0.472	3e-41
Q80W90	388	LIM/homeobox protein Lhx9	no	N/A	0.867	0.438	0.5	7e-41
A0JNI8	397	LIM/homeobox protein Lhx9	no	N/A	0.867	0.428	0.5	1e-40
Q9NQ69	397	LIM/homeobox protein Lhx9	no	N/A	0.867	0.428	0.5	1e-40
A2I8Z7	377	LIM/homeobox protein Lhx9	N/A	N/A	0.867	0.450	0.495	2e-40
Q9WUH2	397	LIM/homeobox protein Lhx9	no	N/A	0.867	0.428	0.5	2e-40
Q1LWV4	396	LIM/homeobox protein Lhx9	no	N/A	0.867	0.429	0.49	2e-40
Q90881	397	LIM/homeobox protein Lhx9	no	N/A	0.867	0.428	0.485	4e-39

>sp|Q9Z0S2|LHX2_MOUSE LIM/homeobox protein Lhx2 OS=Mus musculus GN=Lhx2 PE=1 SV=1

 Score =  169 bits (428), Expect = 1e-41,   Method: Compositional matrix adjust.
 Identities = 105/221 (47%), Positives = 126/221 (57%), Gaps = 55/221 (24%)

Query: 1   MGISSSELVMRARDLVFHLHCFTCISCGILLTKGDLFGMRDEMIYCRPHYEILRHRDY-- 58
           +GIS+SE+VMRARDLV+HL+CFTC +C  +LT GD FGM+D ++YCR H+E L   +Y  
Sbjct: 120 LGISASEMVMRARDLVYHLNCFTCTTCNKMLTTGDHFGMKDSLVYCRLHFEALLQGEYPA 179

Query: 59  ---------------------CGSAEIEQPMSPRPAPWQPT--TVQKGRPRKRKLSVDSP 95
                                 GSA      +P   P+     TVQKGRPRKRK    SP
Sbjct: 180 HFNHADVAAAAAAAAAAKSAGLGSAGA----NPLGLPYYNGVGTVQKGRPRKRK----SP 231

Query: 96  TPPSEDINANVMRIPSTTLEMLHSGDLSSSMESLSY-ESGAGNSSPGSGVHSHQRTKRMR 154
            P                       DL++   +LS  E+ A +        S Q+TKRMR
Sbjct: 232 GP---------------------GADLAAYNAALSCNENDAEHLDRDQPYPSSQKTKRMR 270

Query: 155 TSFKHHQLRTMKSYFNINQNPDAKDLKQLAQKTGLSKRVLQ 195
           TSFKHHQLRTMKSYF IN NPDAKDLKQLAQKTGL+KRVLQ
Sbjct: 271 TSFKHHQLRTMKSYFAINHNPDAKDLKQLAQKTGLTKRVLQ 311

Acts as a transcriptional activator. Stimulates the promoter of the alpha-glycoprotein gene. Transcriptional regulatory protein involved in the control of cell differentiation in developing lymphoid and neural cell types.
Mus musculus (taxid: 10090)

>sp|P50458|LHX2_HUMAN LIM/homeobox protein Lhx2 OS=Homo sapiens GN=LHX2 PE=2 SV=2

 Score =  169 bits (427), Expect = 2e-41,   Method: Compositional matrix adjust.
 Identities = 102/217 (47%), Positives = 124/217 (57%), Gaps = 47/217 (21%)

Query: 1   MGISSSELVMRARDLVFHLHCFTCISCGILLTKGDLFGMRDEMIYCRPHYEILRHRDYCG 60
           +GIS+SE+VMRARDLV+HL+CFTC +C  +LT GD FGM+D ++YCR H+E L   +Y  
Sbjct: 120 LGISASEMVMRARDLVYHLNCFTCTTCNKMLTTGDHFGMKDSLVYCRLHFEALLQGEYPA 179

Query: 61  -------------------SAEIEQPMSPRPAPWQPT--TVQKGRPRKRKLSVDSPTPPS 99
                              +       +P   P+     TVQKGRPRKRK    SP P  
Sbjct: 180 HFNHADVAAAAAAAAAAKSAGLGAAGANPLGLPYYNGVGTVQKGRPRKRK----SPGP-- 233

Query: 100 EDINANVMRIPSTTLEMLHSGDLSSSMESLSY-ESGAGNSSPGSGVHSHQRTKRMRTSFK 158
                                DL++   +LS  E+ A +        S Q+TKRMRTSFK
Sbjct: 234 -------------------GADLAAYNAALSCNENDAEHLDRDQPYPSSQKTKRMRTSFK 274

Query: 159 HHQLRTMKSYFNINQNPDAKDLKQLAQKTGLSKRVLQ 195
           HHQLRTMKSYF IN NPDAKDLKQLAQKTGL+KRVLQ
Sbjct: 275 HHQLRTMKSYFAINHNPDAKDLKQLAQKTGLTKRVLQ 311

Acts as a transcriptional activator. Stimulates the promoter of the alpha-glycoprotein gene. Transcriptional regulatory protein involved in the control of cell differentiation in developing lymphoid and neural cell types.

Homo sapiens (taxid: 9606)

>sp|P36198|LHX2_RAT LIM/homeobox protein Lhx2 OS=Rattus norvegicus GN=Lhx2 PE=2 SV=1

 Score =  167 bits (424), Expect = 3e-41,   Method: Compositional matrix adjust.
 Identities = 102/216 (47%), Positives = 121/216 (56%), Gaps = 46/216 (21%)

Query: 1   MGISSSELVMRARDLVFHLHCFTCISCGILLTKGDLFGMRDEMIYCRPHYEILRHRDY-- 58
           +GIS SE+VMRARDLV+HL+CFTC +C  +LT GD FGM+D ++YCR H+E L   +Y  
Sbjct: 119 LGISESEMVMRARDLVYHLNCFTCTTCNKMLTTGDHFGMKDSLVYCRLHFEALLQGEYPP 178

Query: 59  -----CGSAEIEQPMSPRPAPWQPT-------------TVQKGRPRKRKLSVDSPTPPSE 100
                  +         R   W                TVQKGRPRKRK    SP P   
Sbjct: 179 HFNHADVARAAAAAEQLRVQDWAQLGLTLGLPYYNGVGTVQKGRPRKRK----SPGP--- 231

Query: 101 DINANVMRIPSTTLEMLHSGDLSSSMESLSY-ESGAGNSSPGSGVHSHQRTKRMRTSFKH 159
                               DL++   +LS  E+ A +        S Q+TKRMRTSFKH
Sbjct: 232 ------------------GADLAAYNAALSCNENDAEHLDRDQPYPSSQKTKRMRTSFKH 273

Query: 160 HQLRTMKSYFNINQNPDAKDLKQLAQKTGLSKRVLQ 195
           HQLRTMKSYF IN NPDAKDLKQLAQKTGL+KRVLQ
Sbjct: 274 HQLRTMKSYFAINHNPDAKDLKQLAQKTGLTKRVLQ 309

Acts as a transcriptional activator. Stimulates the promoter of the alpha-glycoprotein gene. Transcriptional regulatory protein involved in the control of cell differentiation in developing lymphoid and neural cell types.

Rattus norvegicus (taxid: 10116)

>sp|Q80W90|LHX9_RAT LIM/homeobox protein Lhx9 OS=Rattus norvegicus GN=Lhx9 PE=2 SV=1

 Score =  166 bits (421), Expect = 7e-41,   Method: Compositional matrix adjust.
 Identities = 100/200 (50%), Positives = 119/200 (59%), Gaps = 30/200 (15%)

Query: 1   MGISSSELVMRARDLVFHLHCFTCISCGILLTKGDLFGMRDEMIYCRPHYEILRHRDY-- 58
           +GIS+SE+VMRARD V+HL CFTC +C   LT GD FGM+D ++YCR H+E L   +Y  
Sbjct: 129 LGISASEMVMRARDSVYHLSCFTCSTCNKTLTTGDHFGMKDSLVYCRAHFETLLQGEYPP 188

Query: 59  -CGSAEIEQPMSPRPAPW--QPTTVQKGRPRKRKLSVDSPTPPSEDINANVMRIPSTTLE 115
                E+         P+     TVQKGRPRKRK    SP    + +N N          
Sbjct: 189 QLSYTELAAKSGGLALPYFNGTGTVQKGRPRKRK----SPALGVDIVNYN---------- 234

Query: 116 MLHSGDLSSSMESLSYESGAGNSSPGSGVHSHQRTKRMRTSFKHHQLRTMKSYFNINQNP 175
              SG   +  + L  +       P S     Q+TKRMRTSFKHHQLRTMKSYF IN NP
Sbjct: 235 ---SGCNENEADHLDRDQ---QPYPPS-----QKTKRMRTSFKHHQLRTMKSYFAINHNP 283

Query: 176 DAKDLKQLAQKTGLSKRVLQ 195
           DAKDLKQLAQKTGL+KRVLQ
Sbjct: 284 DAKDLKQLAQKTGLTKRVLQ 303

Involved in gonadal development.

Rattus norvegicus (taxid: 10116)

>sp|A0JNI8|LHX9_BOVIN LIM/homeobox protein Lhx9 OS=Bos taurus GN=LHX9 PE=2 SV=2

 Score =  166 bits (420), Expect = 1e-40,   Method: Compositional matrix adjust.
 Identities = 100/200 (50%), Positives = 119/200 (59%), Gaps = 30/200 (15%)

Query: 1   MGISSSELVMRARDLVFHLHCFTCISCGILLTKGDLFGMRDEMIYCRPHYEILRHRDY-- 58
           +GIS+SE+VMRARD V+HL CFTC +C   LT GD FGM+D ++YCR H+E L   +Y  
Sbjct: 138 LGISASEMVMRARDSVYHLSCFTCSTCNKTLTTGDHFGMKDSLVYCRAHFETLLQGEYPP 197

Query: 59  -CGSAEIEQPMSPRPAPW--QPTTVQKGRPRKRKLSVDSPTPPSEDINANVMRIPSTTLE 115
                E+         P+     TVQKGRPRKRK    SP    + +N N          
Sbjct: 198 QLSYTELAAKSGGLALPYFNGTGTVQKGRPRKRK----SPALGVDIVNYN---------- 243

Query: 116 MLHSGDLSSSMESLSYESGAGNSSPGSGVHSHQRTKRMRTSFKHHQLRTMKSYFNINQNP 175
              SG   +  + L  +       P S     Q+TKRMRTSFKHHQLRTMKSYF IN NP
Sbjct: 244 ---SGCNENEADHLDRDQ---QPYPPS-----QKTKRMRTSFKHHQLRTMKSYFAINHNP 292

Query: 176 DAKDLKQLAQKTGLSKRVLQ 195
           DAKDLKQLAQKTGL+KRVLQ
Sbjct: 293 DAKDLKQLAQKTGLTKRVLQ 312

Involved in gonadal development.

Bos taurus (taxid: 9913)

>sp|Q9NQ69|LHX9_HUMAN LIM/homeobox protein Lhx9 OS=Homo sapiens GN=LHX9 PE=1 SV=3

 Score =  166 bits (420), Expect = 1e-40,   Method: Compositional matrix adjust.
 Identities = 100/200 (50%), Positives = 119/200 (59%), Gaps = 30/200 (15%)

Query: 1   MGISSSELVMRARDLVFHLHCFTCISCGILLTKGDLFGMRDEMIYCRPHYEILRHRDY-- 58
           +GIS+SE+VMRARD V+HL CFTC +C   LT GD FGM+D ++YCR H+E L   +Y  
Sbjct: 138 LGISASEMVMRARDSVYHLSCFTCSTCNKTLTTGDHFGMKDSLVYCRAHFETLLQGEYPP 197

Query: 59  -CGSAEIEQPMSPRPAPW--QPTTVQKGRPRKRKLSVDSPTPPSEDINANVMRIPSTTLE 115
                E+         P+     TVQKGRPRKRK    SP    + +N N          
Sbjct: 198 QLSYTELAAKSGGLALPYFNGTGTVQKGRPRKRK----SPALGVDIVNYN---------- 243

Query: 116 MLHSGDLSSSMESLSYESGAGNSSPGSGVHSHQRTKRMRTSFKHHQLRTMKSYFNINQNP 175
              SG   +  + L  +       P S     Q+TKRMRTSFKHHQLRTMKSYF IN NP
Sbjct: 244 ---SGCNENEADHLDRDQ---QPYPPS-----QKTKRMRTSFKHHQLRTMKSYFAINHNP 292

Query: 176 DAKDLKQLAQKTGLSKRVLQ 195
           DAKDLKQLAQKTGL+KRVLQ
Sbjct: 293 DAKDLKQLAQKTGLTKRVLQ 312

Involved in gonadal development.

Homo sapiens (taxid: 9606)

>sp|A2I8Z7|LHX9_ASTFA LIM/homeobox protein Lhx9 OS=Astyanax fasciatus GN=lhx9 PE=2 SV=1

 Score =  165 bits (418), Expect = 2e-40,   Method: Compositional matrix adjust.
 Identities = 99/200 (49%), Positives = 119/200 (59%), Gaps = 30/200 (15%)

Query: 1   MGISSSELVMRARDLVFHLHCFTCISCGILLTKGDLFGMRDEMIYCRPHYEILRHRDY-- 58
           +GIS+SE+VMRARD V+HL CFTC SC   LT GD FGMR+ ++YCR H+E L   +Y  
Sbjct: 119 LGISASEMVMRARDSVYHLSCFTCTSCNKTLTTGDHFGMRENLVYCRAHFESLVQGEYHA 178

Query: 59  -CGSAEIEQPMSPRPAPW--QPTTVQKGRPRKRKLSVDSPTPPSEDINANVMRIPSTTLE 115
               AE+         P+    + VQKGRPRKRK        P+  I+ N          
Sbjct: 179 PLNYAELAAKGGGLALPYFNGASAVQKGRPRKRK-------SPAMGIDINT--------- 222

Query: 116 MLHSGDLSSSMESLSYESGAGNSSPGSGVHSHQRTKRMRTSFKHHQLRTMKSYFNINQNP 175
             +SG   +  + L  +       P S     Q+TK MRTSFKHHQLRTMKSYF IN NP
Sbjct: 223 -YNSGCNENDADHLDRDQ---QPYPPS-----QKTKXMRTSFKHHQLRTMKSYFAINHNP 273

Query: 176 DAKDLKQLAQKTGLSKRVLQ 195
           DAKDLKQLAQKTGL+KRVLQ
Sbjct: 274 DAKDLKQLAQKTGLTKRVLQ 293

May be involved in gonadal development.

Astyanax fasciatus (taxid: 223369)

>sp|Q9WUH2|LHX9_MOUSE LIM/homeobox protein Lhx9 OS=Mus musculus GN=Lhx9 PE=1 SV=3

 Score =  165 bits (418), Expect = 2e-40,   Method: Compositional matrix adjust.
 Identities = 100/200 (50%), Positives = 119/200 (59%), Gaps = 30/200 (15%)

Query: 1   MGISSSELVMRARDLVFHLHCFTCISCGILLTKGDLFGMRDEMIYCRPHYEILRHRDY-- 58
           +GIS+SE+VMRARD V+HL CFTC +C   LT GD FGM+D ++YCR H+E L   +Y  
Sbjct: 138 LGISASEMVMRARDSVYHLSCFTCSTCNKTLTTGDHFGMKDSLVYCRAHFETLLQGEYPP 197

Query: 59  -CGSAEIEQPMSPRPAPW--QPTTVQKGRPRKRKLSVDSPTPPSEDINANVMRIPSTTLE 115
                E+         P+     TVQKGRPRKRK    SP    + +N N          
Sbjct: 198 QLSYTELAAKSGGLALPYFNGTGTVQKGRPRKRK----SPALGVDIVNYN---------- 243

Query: 116 MLHSGDLSSSMESLSYESGAGNSSPGSGVHSHQRTKRMRTSFKHHQLRTMKSYFNINQNP 175
              SG   +  + L  +       P S     Q+TKRMRTSFKHHQLRTMKSYF IN NP
Sbjct: 244 ---SGCNENEADHLDRDQ---QPYPPS-----QKTKRMRTSFKHHQLRTMKSYFAINHNP 292

Query: 176 DAKDLKQLAQKTGLSKRVLQ 195
           DAKDLKQLAQKTGL+KRVLQ
Sbjct: 293 DAKDLKQLAQKTGLTKRVLQ 312

Involved in gonadal development.

Mus musculus (taxid: 10090)

>sp|Q1LWV4|LHX9_DANRE LIM/homeobox protein Lhx9 OS=Danio rerio GN=lhx9 PE=2 SV=1

 Score =  165 bits (417), Expect = 2e-40,   Method: Compositional matrix adjust.
 Identities = 98/200 (49%), Positives = 116/200 (58%), Gaps = 30/200 (15%)

Query: 1   MGISSSELVMRARDLVFHLHCFTCISCGILLTKGDLFGMRDEMIYCRPHYEILRHRDY-- 58
           +GIS+SE+VMRARD V+HL CFTC +C   LT GD FGM+D ++YCR H+E L   +Y  
Sbjct: 138 LGISASEMVMRARDSVYHLSCFTCTTCNKTLTTGDHFGMKDNLVYCRVHFETLIQGEYHP 197

Query: 59  -CGSAEIEQPMSPRPAPW--QPTTVQKGRPRKRKLSVDSPTPPSEDINANVMRIPSTTLE 115
               AE+         P+     TVQKGRPRKRK        P+  I+            
Sbjct: 198 QLNYAELAAKGGGLALPYFNGTGTVQKGRPRKRK-------SPAMGIDI----------- 239

Query: 116 MLHSGDLSSSMESLSYESGAGNSSPGSGVHSHQRTKRMRTSFKHHQLRTMKSYFNINQNP 175
               G  SS       +    +  P       Q+TKRMRTSFKHHQLRTMKSYF IN NP
Sbjct: 240 ----GSYSSGCNENDADHLDRDQQP---YPPSQKTKRMRTSFKHHQLRTMKSYFAINHNP 292

Query: 176 DAKDLKQLAQKTGLSKRVLQ 195
           DAKDLKQLAQKTGL+KRVLQ
Sbjct: 293 DAKDLKQLAQKTGLTKRVLQ 312

May be involved in gonadal development.

Danio rerio (taxid: 7955)

>sp|Q90881|LHX9_CHICK LIM/homeobox protein Lhx9 OS=Gallus gallus GN=LHX9 PE=2 SV=2

 Score =  160 bits (406), Expect = 4e-39,   Method: Compositional matrix adjust.
 Identities = 97/200 (48%), Positives = 118/200 (59%), Gaps = 30/200 (15%)

Query: 1   MGISSSELVMRARDLVFHLHCFTCISCGILLTKGDLFGMRDEMIYCRPHYEILRHRDY-- 58
           +GIS+SE+VMRAR+ V+HL CFTC +C   LT GD FGM+D ++YCR H+E L   +Y  
Sbjct: 138 LGISASEMVMRARESVYHLSCFTCTTCNKTLTTGDHFGMKDNLVYCRAHFESLLQGEYPP 197

Query: 59  -CGSAEIEQPMSPRPAPW--QPTTVQKGRPRKRKLSVDSPTPPSEDINANVMRIPSTTLE 115
                E+         P+     TVQKGRPRKRK    SP    + +N N          
Sbjct: 198 QLSYTELAAKSGGLALPYFNGTGTVQKGRPRKRK----SPALGVDIVNYN---------- 243

Query: 116 MLHSGDLSSSMESLSYESGAGNSSPGSGVHSHQRTKRMRTSFKHHQLRTMKSYFNINQNP 175
              SG   +  + +  +       P S     Q+TKRM TSFKHHQLRTMKSYF IN NP
Sbjct: 244 ---SGCNENEADHMDRDQ---QPYPPS-----QKTKRMATSFKHHQLRTMKSYFAINHNP 292

Query: 176 DAKDLKQLAQKTGLSKRVLQ 195
           DAKDLKQLAQKTGL+KRVLQ
Sbjct: 293 DAKDLKQLAQKTGLTKRVLQ 312

May be involved in gonadal development.

Gallus gallus (taxid: 9031)

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Length	Definition	Q cover	H cover	Identity	E-value
Query	196
357622661	359	apterous [Danaus plexippus]	0.959	0.523	0.608	2e-59
380690603	231	apterous, partial [Cydia pomonella]	0.918	0.779	0.641	7e-59
328925124	349	apterous B alpha [Bombyx mori]	0.954	0.535	0.603	2e-57
225543484	361	apterous [Tribolium castaneum] gi|224459	0.933	0.506	0.607	8e-57
328787166	390	PREDICTED: LIM/homeobox protein Lhx9-lik	0.938	0.471	0.603	1e-56
383850874	391	PREDICTED: LIM/homeobox protein Lhx9-lik	0.938	0.470	0.603	4e-56
380027052	390	PREDICTED: LIM/homeobox protein Lhx9-lik	0.948	0.476	0.609	8e-56
242023961	383	LIM/homeobox protein Lhx2, putative [Ped	0.948	0.485	0.589	2e-55
350404759	441	PREDICTED: LIM/homeobox protein Lhx9-lik	0.938	0.417	0.594	4e-55
340721020	391	PREDICTED: LIM/homeobox protein Lhx9-lik	0.938	0.470	0.594	5e-55

>gi|357622661|gb|EHJ74087.1| apterous [Danaus plexippus]

 Score =  233 bits (595), Expect = 2e-59,   Method: Compositional matrix adjust.
 Identities = 123/202 (60%), Positives = 149/202 (73%), Gaps = 14/202 (6%)

Query: 2   GISSSELVMRARDLVFHLHCFTCISCGILLTKGDLFGMRDEMIYCRPHYEILRHRDYC-- 59
           GI+++ELVMRARD+VFHL CFTC++CG LL+KGD+FGMR+ ++YCRPHY+ +   D+C  
Sbjct: 86  GITANELVMRARDMVFHLTCFTCVACGTLLSKGDVFGMRNSLVYCRPHYDSVCMDDFCEE 145

Query: 60  --GSAEIEQPMSPR---PAPWQPTTV-QKGRPRKRKLSVDSPTPPSEDINANVMRIPSTT 113
              S    Q ++     P  + P  V QKGRPRKRK++      P ED+    MR+ ST 
Sbjct: 146 DVNSVYRCQELNSEGDSPNQYFPVGVNQKGRPRKRKIA----HGPHEDMQVQTMRMASTA 201

Query: 114 LEMLHSGDLSSSMESLSYESGAGNSSPGSGVHSHQRTKRMRTSFKHHQLRTMKSYFNINQ 173
           L++LH  DLSSSMESL+Y+S    +SPGS     QRTKRMRTSFKHHQLRTMKSYF INQ
Sbjct: 202 LDILHRADLSSSMESLAYDSSV--ASPGSVSSHTQRTKRMRTSFKHHQLRTMKSYFAINQ 259

Query: 174 NPDAKDLKQLAQKTGLSKRVLQ 195
           NPDAKDLKQLAQKTGLSKRVLQ
Sbjct: 260 NPDAKDLKQLAQKTGLSKRVLQ 281

Source: Danaus plexippus

Species: Danaus plexippus

Genus: Danaus

Family: Nymphalidae

Order: Lepidoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|380690603|gb|AFD93370.1| apterous, partial [Cydia pomonella]

 Score =  232 bits (591), Expect = 7e-59,   Method: Compositional matrix adjust.
 Identities = 127/198 (64%), Positives = 148/198 (74%), Gaps = 18/198 (9%)

Query: 2   GISSSELVMRARDLVFHLHCFTCISCGILLTKGDLFGMRDEMIYCRPHYEILRHRDYCGS 61
           GI+++ELVMRARD V+HL CF+C +CG LL+KGD+FGMRD ++YCRPHYE     D   S
Sbjct: 47  GITANELVMRARDAVYHLTCFSCAACGSLLSKGDVFGMRDNLVYCRPHYEQEYDDD---S 103

Query: 62  AEIEQPMSPRPAPWQ----PTTVQKGRPRKRKLSVDSPTPPSEDINANVMRIPSTTLEML 117
               Q M    +P Q    P+  QKGRPRKRKL+  SP    +D+    MR+ ST LE+L
Sbjct: 104 VYRCQEMDSEGSPSQFYGGPS--QKGRPRKRKLA-QSP----DDMQVQTMRMASTALEIL 156

Query: 118 HSGDLSSSMESLSYESGAGNSSPGSGVHSHQRTKRMRTSFKHHQLRTMKSYFNINQNPDA 177
           H GDLSSSMESL+Y+SGA  +SPGS   S  RTKRMRTSFKHHQLRTMKSYF +NQNPDA
Sbjct: 157 HRGDLSSSMESLAYDSGA--ASPGS--VSSTRTKRMRTSFKHHQLRTMKSYFAVNQNPDA 212

Query: 178 KDLKQLAQKTGLSKRVLQ 195
           KDLKQLAQKTGLSKRVLQ
Sbjct: 213 KDLKQLAQKTGLSKRVLQ 230

Source: Cydia pomonella

Species: Cydia pomonella

Genus: Cydia

Family: Tortricidae

Order: Lepidoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|328925124|dbj|BAK19077.1| apterous B alpha [Bombyx mori]

 Score =  227 bits (578), Expect = 2e-57,   Method: Compositional matrix adjust.
 Identities = 122/202 (60%), Positives = 148/202 (73%), Gaps = 15/202 (7%)

Query: 2   GISSSELVMRARDLVFHLHCFTCISCGILLTKGDLFGMRDEMIYCRPHYEILRHRDYCGS 61
           GI+++ELVMRARDLV+HL+CFTC++CG  L+KGD+FGM+  ++YCRPHY+     DYC  
Sbjct: 86  GITANELVMRARDLVYHLNCFTCVACGTQLSKGDVFGMKGGLVYCRPHYDTACLDDYCDE 145

Query: 62  AEIE----QPM---SPRPAPWQPTTVQKGRPRKRKLSVDSPTPPSEDINANVMRIPSTTL 114
                   Q M      P  +   +  KGRPRKRK+   SP    +++ A  +R+ S+ L
Sbjct: 146 EMTNGYRCQDMHNGGNSPQYYSGGSTPKGRPRKRKIPHGSP----DELQAQTIRMASSAL 201

Query: 115 EMLHSGDLSSSMESLSYESGAGNSSPGSGVHSH-QRTKRMRTSFKHHQLRTMKSYFNINQ 173
           E+LH GDLSSSMESL+Y+S    +SPGS V SH QRTKRMRTSFKHHQLRTMKSYF INQ
Sbjct: 202 EILHRGDLSSSMESLAYDSSV--ASPGS-VSSHTQRTKRMRTSFKHHQLRTMKSYFAINQ 258

Query: 174 NPDAKDLKQLAQKTGLSKRVLQ 195
           NPDAKDLKQLAQKTGLSKRVLQ
Sbjct: 259 NPDAKDLKQLAQKTGLSKRVLQ 280

Source: Bombyx mori

Species: Bombyx mori

Genus: Bombyx

Family: Bombycidae

Order: Lepidoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|225543484|ref|NP_001139388.1| apterous [Tribolium castaneum] gi|224459214|gb|ACN43342.1| apterous b [Tribolium castaneum]

 Score =  225 bits (573), Expect = 8e-57,   Method: Compositional matrix adjust.
 Identities = 124/204 (60%), Positives = 145/204 (71%), Gaps = 21/204 (10%)

Query: 2   GISSSELVMRARDLVFHLHCFTCISCGILLTKGDLFGMRDEMIYCRPHYEILRHRDYCGS 61
           GIS++ELVMRARD V+HLHCF+C SCG+ L+KGD FGMRD +IYCRPHYE+L   D+C +
Sbjct: 98  GISANELVMRARDSVYHLHCFSCTSCGMPLSKGDHFGMRDGLIYCRPHYELL---DFCDT 154

Query: 62  AEIEQPM---SPRPAPWQPTTV---QKGRPRKRKLSVDSPTPPSEDINAN----VMRIPS 111
           ++  + M   S  P  +         KGRPRKRKL       P ED         MR+ +
Sbjct: 155 SDPVEMMFRGSESPPGYFANAAPQHHKGRPRKRKL-------PVEDRGCGEIPVTMRMAA 207

Query: 112 TTLEMLHSGDLSSSMESLSYESGAGNSSPGSGVHSHQRTKRMRTSFKHHQLRTMKSYFNI 171
            TLEML  GDLSSSMESLSY+S   + +  +G H  QRTKRMRTSFKHHQLRTMK+YF I
Sbjct: 208 ATLEMLQQGDLSSSMESLSYDSSVTSPASSNG-HQPQRTKRMRTSFKHHQLRTMKTYFAI 266

Query: 172 NQNPDAKDLKQLAQKTGLSKRVLQ 195
           NQNPDAKDLKQLAQKTGLSKRVLQ
Sbjct: 267 NQNPDAKDLKQLAQKTGLSKRVLQ 290

Source: Tribolium castaneum

Species: Tribolium castaneum

Genus: Tribolium

Family: Tenebrionidae

Order: Coleoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|328787166|ref|XP_003250891.1| PREDICTED: LIM/homeobox protein Lhx9-like [Apis mellifera]

 Score =  224 bits (572), Expect = 1e-56,   Method: Compositional matrix adjust.
 Identities = 128/212 (60%), Positives = 148/212 (69%), Gaps = 28/212 (13%)

Query: 2   GISSSELVMRARDLVFHLHCFTCISCGILLTKGDLFGMRDEMIYCRPHYEILR-HRDYCG 60
           GIS++ELVMRARDLV+H+ CFTC SCG  L KGD FG RD ++YCRPHYE+L    DY G
Sbjct: 105 GISATELVMRARDLVYHVACFTCASCGTPLNKGDYFGQRDGLVYCRPHYELLCCAGDYGG 164

Query: 61  SA----EIEQP-MSPRPAPWQPT---------TVQKGRPRKRKLS--VDSPTPPSEDINA 104
           +A    +I  P +SP PA +            TVQKGRPRKRKLS    S  P +     
Sbjct: 165 AATSIEDIGSPGVSPLPAYYSAAEQSPITSSGTVQKGRPRKRKLSEVTGSELPVT----- 219

Query: 105 NVMRIPSTTLEMLHSGDLSSSMESLS-YESGAGNSSPGSGVHSHQRTKRMRTSFKHHQLR 163
             MR+ +  LE+LH  +LSSSMESL+ YE+  G+  P   VH  QRTKRMRTSFKHHQLR
Sbjct: 220 --MRLAAGALELLHPTELSSSMESLAAYEASVGSPGP---VHQSQRTKRMRTSFKHHQLR 274

Query: 164 TMKSYFNINQNPDAKDLKQLAQKTGLSKRVLQ 195
           TMK+YF INQNPDAKDLKQLAQKTGLSKRVLQ
Sbjct: 275 TMKNYFAINQNPDAKDLKQLAQKTGLSKRVLQ 306

Source: Apis mellifera

Species: Apis mellifera

Genus: Apis

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|383850874|ref|XP_003700999.1| PREDICTED: LIM/homeobox protein Lhx9-like [Megachile rotundata]

 Score =  223 bits (567), Expect = 4e-56,   Method: Compositional matrix adjust.
 Identities = 128/212 (60%), Positives = 146/212 (68%), Gaps = 28/212 (13%)

Query: 2   GISSSELVMRARDLVFHLHCFTCISCGILLTKGDLFGMRDEMIYCRPHYEILRHRDYCGS 61
           GIS+SELVMRARDLV+H+ CFTC SCG  L KGD FG RD ++YCRPHYE+L      GS
Sbjct: 106 GISASELVMRARDLVYHVACFTCASCGTPLNKGDHFGQRDGLVYCRPHYELLCCAGDYGS 165

Query: 62  A-----EIEQP-MSPRPAPWQPT---------TVQKGRPRKRKLS--VDSPTPPSEDINA 104
           A     +I  P +SP PA +            TVQKGRPRKRKLS    S  P +     
Sbjct: 166 AASNIEDIGSPGVSPLPAYYSAAEQSPIATSGTVQKGRPRKRKLSEVTGSELPVT----- 220

Query: 105 NVMRIPSTTLEMLHSGDLSSSMESLS-YESGAGNSSPGSGVHSHQRTKRMRTSFKHHQLR 163
             MR+ +  LE+LH  +LSSSMESL+ YE+  G+  P   VH  QRTKRMRTSFKHHQLR
Sbjct: 221 --MRLAAGALELLHPTELSSSMESLAAYEASVGSPGP---VHQSQRTKRMRTSFKHHQLR 275

Query: 164 TMKSYFNINQNPDAKDLKQLAQKTGLSKRVLQ 195
           TMK+YF INQNPDAKDLKQLAQKTGLSKRVLQ
Sbjct: 276 TMKNYFAINQNPDAKDLKQLAQKTGLSKRVLQ 307

Source: Megachile rotundata

Species: Megachile rotundata

Genus: Megachile

Family: Megachilidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|380027052|ref|XP_003697250.1| PREDICTED: LIM/homeobox protein Lhx9-like [Apis florea]

 Score =  221 bits (564), Expect = 8e-56,   Method: Compositional matrix adjust.
 Identities = 128/210 (60%), Positives = 149/210 (70%), Gaps = 24/210 (11%)

Query: 2   GISSSELVMRARDLVFHLHCFTCISCGILLTKGDLFGMRDEMIYCRPHYEILR-HRDYCG 60
           GIS++ELVMRARDLV+H+ CFTC SCG  L KGD FG RD ++YCRPHYE+L    DY G
Sbjct: 105 GISATELVMRARDLVYHVACFTCASCGTPLNKGDHFGQRDGLVYCRPHYELLCCAGDYGG 164

Query: 61  SA----EIEQP-MSPRPAPWQ-----PTT----VQKGRPRKRKLSVDSPTPPSEDINANV 106
           +A    +I  P +SP PA +      P T    VQKGRPRKRKLS  +      D+    
Sbjct: 165 AATSIEDIGSPGVSPLPAYYSAAEQSPITSSGAVQKGRPRKRKLSEVT----GSDLPV-T 219

Query: 107 MRIPSTTLEMLHSGDLSSSMESLS-YESGAGNSSPGSGVHSHQRTKRMRTSFKHHQLRTM 165
           MR+ +  LE+LH  +LSSSMESL+ YE+  G+  P   VH  QRTKRMRTSFKHHQLRTM
Sbjct: 220 MRLAAGALELLHPTELSSSMESLAAYEASVGSPGP---VHQSQRTKRMRTSFKHHQLRTM 276

Query: 166 KSYFNINQNPDAKDLKQLAQKTGLSKRVLQ 195
           K+YF INQNPDAKDLKQLAQKTGLSKRVLQ
Sbjct: 277 KNYFAINQNPDAKDLKQLAQKTGLSKRVLQ 306

Source: Apis florea

Species: Apis florea

Genus: Apis

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|242023961|ref|XP_002432399.1| LIM/homeobox protein Lhx2, putative [Pediculus humanus corporis] gi|212517822|gb|EEB19661.1| LIM/homeobox protein Lhx2, putative [Pediculus humanus corporis]

 Score =  220 bits (561), Expect = 2e-55,   Method: Compositional matrix adjust.
 Identities = 119/202 (58%), Positives = 141/202 (69%), Gaps = 16/202 (7%)

Query: 2   GISSSELVMRARDLVFHLHCFTCISCGILLTKGDLFGMRDEMIYCRPHYE-ILRHRDYCG 60
           GIS+SELVMRA+D+VFH++CFTC SCGI L+KGD FGMR+ ++YC PHYE +  H  YC 
Sbjct: 99  GISASELVMRAKDMVFHINCFTCTSCGIPLSKGDHFGMRNGLVYCHPHYEHLCSHDPYCN 158

Query: 61  SAEIEQPMSPRPAPWQPTT-------VQKGRPRKRKLSVDSPTPPSEDINANVMRIPSTT 113
             +        PA +  T        VQKGRPRKRKL     + P  D+N + +R+ + T
Sbjct: 159 DLDNVFRAGGSPADFYNTGNDRISGGVQKGRPRKRKLQTPIDSSPGSDLNVS-LRLSTAT 217

Query: 114 LEMLHSGDLSSSMESLSYESGAGNSSPGSGVHSHQRTKRMRTSFKHHQLRTMKSYFNINQ 173
           LEMLH  +LSSSM+S+SY+           V S Q TKRMRTSFKHHQLRTMKSYF INQ
Sbjct: 218 LEMLHPNELSSSMDSISYDGPLT-------VPSQQSTKRMRTSFKHHQLRTMKSYFAINQ 270

Query: 174 NPDAKDLKQLAQKTGLSKRVLQ 195
           NPDAKDLKQLAQKTGLSKRVLQ
Sbjct: 271 NPDAKDLKQLAQKTGLSKRVLQ 292

Source: Pediculus humanus corporis

Species: Pediculus humanus

Genus: Pediculus

Family: Pediculidae

Order: Phthiraptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|350404759|ref|XP_003487211.1| PREDICTED: LIM/homeobox protein Lhx9-like [Bombus impatiens]

 Score =  219 bits (559), Expect = 4e-55,   Method: Compositional matrix adjust.
 Identities = 126/212 (59%), Positives = 145/212 (68%), Gaps = 28/212 (13%)

Query: 2   GISSSELVMRARDLVFHLHCFTCISCGILLTKGDLFGMRDEMIYCRPHYEILRHRDYCGS 61
           GI ++ELVMRARDLV+H+ CFTC SCG  L KGD FG RD ++YCRPHYE+L      GS
Sbjct: 156 GIFATELVMRARDLVYHVACFTCASCGTPLNKGDHFGQRDGLVYCRPHYELLCCAGDYGS 215

Query: 62  A-----EIEQP-MSPRPAPWQPT---------TVQKGRPRKRKLS--VDSPTPPSEDINA 104
           A     +I  P +SP PA +            TVQKGRPRKRKLS    S  P +     
Sbjct: 216 AASNIEDIGSPGVSPLPAYYSAAEQSPITSSGTVQKGRPRKRKLSEVTGSELPVT----- 270

Query: 105 NVMRIPSTTLEMLHSGDLSSSMESLS-YESGAGNSSPGSGVHSHQRTKRMRTSFKHHQLR 163
             MR+ +  LE+LH  +LSSSMESL+ YE+  G+  P   VH  QRTKRMRTSFKHHQLR
Sbjct: 271 --MRLAAGALELLHPTELSSSMESLAAYEASVGSPGP---VHQSQRTKRMRTSFKHHQLR 325

Query: 164 TMKSYFNINQNPDAKDLKQLAQKTGLSKRVLQ 195
           TMK+YF INQNPDAKDLKQLAQKTGLSKRVLQ
Sbjct: 326 TMKNYFAINQNPDAKDLKQLAQKTGLSKRVLQ 357

Source: Bombus impatiens

Species: Bombus impatiens

Genus: Bombus

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|340721020|ref|XP_003398925.1| PREDICTED: LIM/homeobox protein Lhx9-like [Bombus terrestris]

 Score =  219 bits (557), Expect = 5e-55,   Method: Compositional matrix adjust.
 Identities = 126/212 (59%), Positives = 145/212 (68%), Gaps = 28/212 (13%)

Query: 2   GISSSELVMRARDLVFHLHCFTCISCGILLTKGDLFGMRDEMIYCRPHYEILRHRDYCGS 61
           GI ++ELVMRARDLV+H+ CFTC SCG  L KGD FG RD ++YCRPHYE+L      GS
Sbjct: 106 GIFATELVMRARDLVYHVACFTCASCGTPLNKGDHFGQRDGLVYCRPHYELLCCAGDYGS 165

Query: 62  A-----EIEQP-MSPRPAPWQPT---------TVQKGRPRKRKLS--VDSPTPPSEDINA 104
           A     +I  P +SP PA +            TVQKGRPRKRKLS    S  P +     
Sbjct: 166 AASNIEDIGSPGVSPLPAYYSAAEQSPITSSGTVQKGRPRKRKLSEVTGSELPVT----- 220

Query: 105 NVMRIPSTTLEMLHSGDLSSSMESLS-YESGAGNSSPGSGVHSHQRTKRMRTSFKHHQLR 163
             MR+ +  LE+LH  +LSSSMESL+ YE+  G+  P   VH  QRTKRMRTSFKHHQLR
Sbjct: 221 --MRLAAGALELLHPTELSSSMESLAAYEASVGSPGP---VHQSQRTKRMRTSFKHHQLR 275

Query: 164 TMKSYFNINQNPDAKDLKQLAQKTGLSKRVLQ 195
           TMK+YF INQNPDAKDLKQLAQKTGLSKRVLQ
Sbjct: 276 TMKNYFAINQNPDAKDLKQLAQKTGLSKRVLQ 307

Source: Bombus terrestris

Species: Bombus terrestris

Genus: Bombus

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	196
UNIPROTKB|E1BM14	406	LHX2 "Uncharacterized protein"	0.255	0.123	0.9	3.6e-43
UNIPROTKB|E2RPC3	406	LHX2 "Uncharacterized protein"	0.255	0.123	0.9	3.6e-43
UNIPROTKB|P50458	406	LHX2 "LIM/homeobox protein Lhx	0.255	0.123	0.9	3.6e-43
UNIPROTKB|C4TJC6	406	Lhx2 "LIM homeobox protein 2"	0.255	0.123	0.9	3.6e-43
MGI|MGI:96785	406	Lhx2 "LIM homeobox protein 2"	0.255	0.123	0.9	3.6e-43
UNIPROTKB|D4A380	406	Lhx2 "LIM/homeobox protein Lhx	0.255	0.123	0.9	3.6e-43
UNIPROTKB|H7C0H1	412	LHX2 "LIM/homeobox protein Lhx	0.255	0.121	0.9	4.4e-43
UNIPROTKB|G3N0G6	427	LHX2 "Uncharacterized protein"	0.255	0.117	0.9	6.6e-43
RGD|71076	426	Lhx2 "LIM homeobox 2" [Rattus	0.255	0.117	0.9	8.1e-43
UNIPROTKB|P36198	426	Lhx2 "LIM/homeobox protein Lhx	0.255	0.117	0.9	8.1e-43

UNIPROTKB|E1BM14 LHX2 "Uncharacterized protein" [Bos taurus (taxid:9913)]

 Score = 230 (86.0 bits), Expect = 3.6e-43, Sum P(3) = 3.6e-43
 Identities = 45/50 (90%), Positives = 47/50 (94%)

Query:   146 SHQRTKRMRTSFKHHQLRTMKSYFNINQNPDAKDLKQLAQKTGLSKRVLQ 195
             S Q+TKRMRTSFKHHQLRTMKSYF IN NPDAKDLKQLAQKTGL+KRVLQ
Sbjct:   262 SSQKTKRMRTSFKHHQLRTMKSYFAINHNPDAKDLKQLAQKTGLTKRVLQ 311

GO:0005634 "nucleus" evidence=IEA

GO:0043565 "sequence-specific DNA binding" evidence=IEA

GO:0008270 "zinc ion binding" evidence=IEA

GO:0003700 "sequence-specific DNA binding transcription factor activity" evidence=IEA

UNIPROTKB|E2RPC3 LHX2 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 230 (86.0 bits), Expect = 3.6e-43, Sum P(3) = 3.6e-43
 Identities = 45/50 (90%), Positives = 47/50 (94%)

Query:   146 SHQRTKRMRTSFKHHQLRTMKSYFNINQNPDAKDLKQLAQKTGLSKRVLQ 195
             S Q+TKRMRTSFKHHQLRTMKSYF IN NPDAKDLKQLAQKTGL+KRVLQ
Sbjct:   262 SSQKTKRMRTSFKHHQLRTMKSYFAINHNPDAKDLKQLAQKTGLTKRVLQ 311

GO:0005634 "nucleus" evidence=IEA

GO:0043565 "sequence-specific DNA binding" evidence=IEA

GO:0008270 "zinc ion binding" evidence=IEA

GO:0003700 "sequence-specific DNA binding transcription factor activity" evidence=IEA

UNIPROTKB|P50458 LHX2 "LIM/homeobox protein Lhx2" [Homo sapiens (taxid:9606)]

 Score = 230 (86.0 bits), Expect = 3.6e-43, Sum P(3) = 3.6e-43
 Identities = 45/50 (90%), Positives = 47/50 (94%)

Query:   146 SHQRTKRMRTSFKHHQLRTMKSYFNINQNPDAKDLKQLAQKTGLSKRVLQ 195
             S Q+TKRMRTSFKHHQLRTMKSYF IN NPDAKDLKQLAQKTGL+KRVLQ
Sbjct:   262 SSQKTKRMRTSFKHHQLRTMKSYFAINHNPDAKDLKQLAQKTGLTKRVLQ 311

GO:0003700 "sequence-specific DNA binding transcription factor activity" evidence=IEA

GO:0008270 "zinc ion binding" evidence=IEA

GO:0006351 "transcription, DNA-dependent" evidence=IEA

GO:0000988 "protein binding transcription factor activity" evidence=IEA

GO:0001843 "neural tube closure" evidence=IEA

GO:0007411 "axon guidance" evidence=IEA

GO:0007498 "mesoderm development" evidence=IEA

GO:0009953 "dorsal/ventral pattern formation" evidence=IEA

GO:0021978 "telencephalon regionalization" evidence=IEA

GO:0043565 "sequence-specific DNA binding" evidence=IEA

GO:0045944 "positive regulation of transcription from RNA polymerase II promoter" evidence=IEA

GO:2000678 "negative regulation of transcription regulatory region DNA binding" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0045893 "positive regulation of transcription, DNA-dependent" evidence=ISS

UNIPROTKB|C4TJC6 Lhx2 "LIM homeobox protein 2" [Sus scrofa (taxid:9823)]

 Score = 230 (86.0 bits), Expect = 3.6e-43, Sum P(3) = 3.6e-43
 Identities = 45/50 (90%), Positives = 47/50 (94%)

Query:   146 SHQRTKRMRTSFKHHQLRTMKSYFNINQNPDAKDLKQLAQKTGLSKRVLQ 195
             S Q+TKRMRTSFKHHQLRTMKSYF IN NPDAKDLKQLAQKTGL+KRVLQ
Sbjct:   262 SSQKTKRMRTSFKHHQLRTMKSYFAINHNPDAKDLKQLAQKTGLTKRVLQ 311

GO:0005634 "nucleus" evidence=IEA

GO:2000678 "negative regulation of transcription regulatory region DNA binding" evidence=IEA

GO:0045944 "positive regulation of transcription from RNA polymerase II promoter" evidence=IEA

GO:0043565 "sequence-specific DNA binding" evidence=IEA

GO:0021978 "telencephalon regionalization" evidence=IEA

GO:0009953 "dorsal/ventral pattern formation" evidence=IEA

GO:0007498 "mesoderm development" evidence=IEA

GO:0007411 "axon guidance" evidence=IEA

GO:0001843 "neural tube closure" evidence=IEA

GO:0000988 "protein binding transcription factor activity" evidence=IEA

GO:0008270 "zinc ion binding" evidence=IEA

GO:0003700 "sequence-specific DNA binding transcription factor activity" evidence=IEA

MGI|MGI:96785 Lhx2 "LIM homeobox protein 2" [Mus musculus (taxid:10090)]

 Score = 230 (86.0 bits), Expect = 3.6e-43, Sum P(3) = 3.6e-43
 Identities = 45/50 (90%), Positives = 47/50 (94%)

Query:   146 SHQRTKRMRTSFKHHQLRTMKSYFNINQNPDAKDLKQLAQKTGLSKRVLQ 195
             S Q+TKRMRTSFKHHQLRTMKSYF IN NPDAKDLKQLAQKTGL+KRVLQ
Sbjct:   262 SSQKTKRMRTSFKHHQLRTMKSYFAINHNPDAKDLKQLAQKTGLTKRVLQ 311

GO:0001076 "RNA polymerase II transcription factor binding transcription factor activity" evidence=IPI

GO:0001843 "neural tube closure" evidence=IMP

GO:0003677 "DNA binding" evidence=IEA

GO:0003700 "sequence-specific DNA binding transcription factor activity" evidence=IEA

GO:0005515 "protein binding" evidence=IPI

GO:0005622 "intracellular" evidence=IDA

GO:0005634 "nucleus" evidence=IDA

GO:0006351 "transcription, DNA-dependent" evidence=IEA

GO:0006355 "regulation of transcription, DNA-dependent" evidence=IEA

GO:0007399 "nervous system development" evidence=IMP

GO:0007411 "axon guidance" evidence=IMP

GO:0007420 "brain development" evidence=IMP

GO:0007498 "mesoderm development" evidence=IMP

GO:0008270 "zinc ion binding" evidence=IEA

GO:0009953 "dorsal/ventral pattern formation" evidence=IMP

GO:0021537 "telencephalon development" evidence=IMP

GO:0021978 "telencephalon regionalization" evidence=IGI;IMP

GO:0022008 "neurogenesis" evidence=IDA

GO:0030182 "neuron differentiation" evidence=IMP

GO:0043565 "sequence-specific DNA binding" evidence=IDA

GO:0045893 "positive regulation of transcription, DNA-dependent" evidence=IDA

GO:0045944 "positive regulation of transcription from RNA polymerase II promoter" evidence=IGI

GO:0046872 "metal ion binding" evidence=IEA

GO:0048646 "anatomical structure formation involved in morphogenesis" evidence=IMP

GO:2000678 "negative regulation of transcription regulatory region DNA binding" evidence=IGI

UNIPROTKB|D4A380 Lhx2 "LIM/homeobox protein Lhx2" [Rattus norvegicus (taxid:10116)]

 Score = 230 (86.0 bits), Expect = 3.6e-43, Sum P(3) = 3.6e-43
 Identities = 45/50 (90%), Positives = 47/50 (94%)

Query:   146 SHQRTKRMRTSFKHHQLRTMKSYFNINQNPDAKDLKQLAQKTGLSKRVLQ 195
             S Q+TKRMRTSFKHHQLRTMKSYF IN NPDAKDLKQLAQKTGL+KRVLQ
Sbjct:   262 SSQKTKRMRTSFKHHQLRTMKSYFAINHNPDAKDLKQLAQKTGLTKRVLQ 311

GO:0003700 "sequence-specific DNA binding transcription factor activity" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0008270 "zinc ion binding" evidence=IEA

GO:0043565 "sequence-specific DNA binding" evidence=IEA

UNIPROTKB|H7C0H1 LHX2 "LIM/homeobox protein Lhx2" [Homo sapiens (taxid:9606)]

 Score = 230 (86.0 bits), Expect = 4.4e-43, Sum P(3) = 4.4e-43
 Identities = 45/50 (90%), Positives = 47/50 (94%)

Query:   146 SHQRTKRMRTSFKHHQLRTMKSYFNINQNPDAKDLKQLAQKTGLSKRVLQ 195
             S Q+TKRMRTSFKHHQLRTMKSYF IN NPDAKDLKQLAQKTGL+KRVLQ
Sbjct:   268 SSQKTKRMRTSFKHHQLRTMKSYFAINHNPDAKDLKQLAQKTGLTKRVLQ 317

GO:0003700 "sequence-specific DNA binding transcription factor activity" evidence=IEA

GO:0008270 "zinc ion binding" evidence=IEA

GO:0043565 "sequence-specific DNA binding" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

UNIPROTKB|G3N0G6 LHX2 "Uncharacterized protein" [Bos taurus (taxid:9913)]

 Score = 230 (86.0 bits), Expect = 6.6e-43, Sum P(3) = 6.6e-43
 Identities = 45/50 (90%), Positives = 47/50 (94%)

Query:   146 SHQRTKRMRTSFKHHQLRTMKSYFNINQNPDAKDLKQLAQKTGLSKRVLQ 195
             S Q+TKRMRTSFKHHQLRTMKSYF IN NPDAKDLKQLAQKTGL+KRVLQ
Sbjct:   262 SSQKTKRMRTSFKHHQLRTMKSYFAINHNPDAKDLKQLAQKTGLTKRVLQ 311

GO:0005634 "nucleus" evidence=IEA

GO:2000678 "negative regulation of transcription regulatory region DNA binding" evidence=IEA

GO:0045944 "positive regulation of transcription from RNA polymerase II promoter" evidence=IEA

GO:0043565 "sequence-specific DNA binding" evidence=IEA

GO:0021978 "telencephalon regionalization" evidence=IEA

GO:0009953 "dorsal/ventral pattern formation" evidence=IEA

GO:0007498 "mesoderm development" evidence=IEA

GO:0007411 "axon guidance" evidence=IEA

GO:0001843 "neural tube closure" evidence=IEA

GO:0000988 "protein binding transcription factor activity" evidence=IEA

GO:0008270 "zinc ion binding" evidence=IEA

GO:0003700 "sequence-specific DNA binding transcription factor activity" evidence=IEA

RGD|71076 Lhx2 "LIM homeobox 2" [Rattus norvegicus (taxid:10116)]

 Score = 230 (86.0 bits), Expect = 8.1e-43, Sum P(3) = 8.1e-43
 Identities = 45/50 (90%), Positives = 47/50 (94%)

Query:   146 SHQRTKRMRTSFKHHQLRTMKSYFNINQNPDAKDLKQLAQKTGLSKRVLQ 195
             S Q+TKRMRTSFKHHQLRTMKSYF IN NPDAKDLKQLAQKTGL+KRVLQ
Sbjct:   260 SSQKTKRMRTSFKHHQLRTMKSYFAINHNPDAKDLKQLAQKTGLTKRVLQ 309

GO:0000988 "protein binding transcription factor activity" evidence=IEA

GO:0001076 "RNA polymerase II transcription factor binding transcription factor activity" evidence=ISO

GO:0001843 "neural tube closure" evidence=IEA;ISO

GO:0003700 "sequence-specific DNA binding transcription factor activity" evidence=IEA

GO:0005622 "intracellular" evidence=ISO

GO:0005634 "nucleus" evidence=IEA;ISO

GO:0006351 "transcription, DNA-dependent" evidence=IEA

GO:0007399 "nervous system development" evidence=ISO

GO:0007411 "axon guidance" evidence=IEA;ISO

GO:0007420 "brain development" evidence=ISO

GO:0007498 "mesoderm development" evidence=IEA;ISO

GO:0008270 "zinc ion binding" evidence=IEA

GO:0009953 "dorsal/ventral pattern formation" evidence=IEA;ISO

GO:0021537 "telencephalon development" evidence=ISO

GO:0021978 "telencephalon regionalization" evidence=IEA;ISO

GO:0022008 "neurogenesis" evidence=ISO

GO:0030182 "neuron differentiation" evidence=IEP;ISO

GO:0043565 "sequence-specific DNA binding" evidence=IEA;ISO

GO:0045893 "positive regulation of transcription, DNA-dependent" evidence=ISO;ISS

GO:0045944 "positive regulation of transcription from RNA polymerase II promoter" evidence=IEA;ISO

GO:0048646 "anatomical structure formation involved in morphogenesis" evidence=ISO

GO:2000678 "negative regulation of transcription regulatory region DNA binding" evidence=IEA;ISO

UNIPROTKB|P36198 Lhx2 "LIM/homeobox protein Lhx2" [Rattus norvegicus (taxid:10116)]

 Score = 230 (86.0 bits), Expect = 8.1e-43, Sum P(3) = 8.1e-43
 Identities = 45/50 (90%), Positives = 47/50 (94%)

Query:   146 SHQRTKRMRTSFKHHQLRTMKSYFNINQNPDAKDLKQLAQKTGLSKRVLQ 195
             S Q+TKRMRTSFKHHQLRTMKSYF IN NPDAKDLKQLAQKTGL+KRVLQ
Sbjct:   260 SSQKTKRMRTSFKHHQLRTMKSYFAINHNPDAKDLKQLAQKTGLTKRVLQ 309

GO:0003700 "sequence-specific DNA binding transcription factor activity" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0008270 "zinc ion binding" evidence=IEA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

No confident hit for EC number transfering in SWISSPROT detected by BLAST

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database

ID	Length	Definition	E-value
Query	196
cd09377	59	cd09377, LIM2_Lhx2_Lhx9, The second LIM domain of	1e-30
cd09474	59	cd09474, LIM2_Lhx2, The second LIM domain of Lhx2	2e-20
cd09475	59	cd09475, LIM2_Lhx9, The second LIM domain of Lhx9	2e-18
pfam00412	58	pfam00412, LIM, LIM domain	4e-14
cd09378	55	cd09378, LIM2_Lmx1a_Lmx1b, The second LIM domain o	3e-13
cd09379	55	cd09379, LIM2_AWH, The second LIM domain of Arrowh	1e-12
pfam00046	57	pfam00046, Homeobox, Homeobox domain	1e-12
smart00132	54	smart00132, LIM, Zinc-binding domain present in Li	2e-12
smart00389	57	smart00389, HOX, Homeodomain	3e-12
cd09471	55	cd09471, LIM2_Isl2, The second LIM domain of Isl2	3e-12
cd09375	56	cd09375, LIM2_Lhx1_Lhx5, The second LIM domain of	2e-11
cd00086	59	cd00086, homeodomain, Homeodomain; DNA binding dom	2e-11
cd09387	55	cd09387, LIM2_LMO4, The second LIM domain of LMO4	3e-11
cd09374	55	cd09374, LIM2_Isl, The second LIM domain of Isl, a	4e-11
cd08368	53	cd08368, LIM, LIM is a small protein-protein inter	7e-11
cd09472	57	cd09472, LIM2_Lhx3b, The second LIM domain of Lhx3	2e-09
cd09376	56	cd09376, LIM2_Lhx3_Lhx4, The second LIM domain of	2e-09
cd09382	55	cd09382, LIM2_Lhx6, The second LIM domain of Lhx6	3e-09
cd09389	55	cd09389, LIM2_LMO1_LMO3, The second LIM domain of	4e-09
cd09383	55	cd09383, LIM2_Lhx7_Lhx8, The second LIM domain of	7e-09
cd09473	56	cd09473, LIM2_Lhx4, The second LIM domain of Lhx4	1e-08
cd09390	55	cd09390, LIM2_dLMO, The second LIM domain of dLMO	1e-07
cd09327	52	cd09327, LIM1_abLIM, The first LIM domain of actin	1e-05
cd09385	56	cd09385, LIM2_LMO2, The second LIM domain of LMO2	3e-05
cd09350	54	cd09350, LIM1_TRIP6, The first LIM domain of Thyro	9e-05
cd09451	53	cd09451, LIM_RIL, The LIM domain of RIL	9e-05
cd09365	54	cd09365, LIM2_LIMK, The second LIM domain of LIMK	2e-04
cd09358	53	cd09358, LIM_Mical_like, The LIM domain of Mical (	5e-04
cd09464	55	cd09464, LIM2_LIMK1, The second LIM domain of LIMK	6e-04
cd09366	55	cd09366, LIM1_Isl, The first LIM domain of Isl, a	0.001
cd09486	53	cd09486, LIM_Eplin_like_1, a LIM domain subfamily	0.001
cd09362	52	cd09362, LIM2_Enigma_like, The second LIM domain o	0.001
cd09414	58	cd09414, LIM1_LIMPETin, The first LIM domain of pr	0.001
cd09392	53	cd09392, LIM2_Lrg1p_like, The second LIM domain of	0.004
cd09360	52	cd09360, LIM_ALP_like, The LIM domain of ALP (acti	0.004
cd09326	53	cd09326, LIM_CRP_like, The LIM domains of Cysteine	0.004

>gnl|CDD|188763 cd09377, LIM2_Lhx2_Lhx9, The second LIM domain of Lhx2 and Lhx9 family

 Score =  106 bits (266), Expect = 1e-30
 Identities = 37/50 (74%), Positives = 43/50 (86%)

Query: 1  MGISSSELVMRARDLVFHLHCFTCISCGILLTKGDLFGMRDEMIYCRPHY 50
          +GIS+SELVMRARDLVFHL+CFTC +C   LTKGD FGMRD ++YCR HY
Sbjct: 10 LGISASELVMRARDLVFHLNCFTCATCNKPLTKGDHFGMRDGLVYCRLHY 59

The second LIM domain of Lhx2 and Lhx9 family: Lhx2 and Lhx9 are highly homologous LHX regulatory proteins. They belong to the LHX protein family, which features two tandem N-terminal LIM domains and a C-terminal DNA binding homeodomain. Members of LHX family are found in the nucleus and act as transcription factors or cofactors. LHX proteins are critical for the development of specialized cells in multiple tissue types, including the nervous system, skeletal muscle, the heart, the kidneys, and endocrine organs, such as the pituitary gland and the pancreas. Although Lhx2 and Lhx9 are highly homologous, they seems to play regulatory roles in different organs. In animals, Lhx2 plays important roles in eye, cerebral cortex, limb, the olfactory organs, and erythrocyte development. Lhx2 gene knockout mice exhibit impaired patterning of the cortical hem and the telencephalon of the developing brain, and a lack of development in olfactory structures. Lhx9 is expressed in several regions of the developing mouse brain, the spinal cord, the pancreas, in limb mesenchyme, and in the urogenital region. Lhx9 plays critical roles in gonad development. Homozygous mice lacking functional Lhx9 alleles exhibit numerous urogenital defects, such as gonadal agenesis, infertility, and undetectable levels of testosterone and estradiol coupled with high FSH levels. Lhx9 null mice are phenotypically female, even those that are genotypically male. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein. Length = 59

>gnl|CDD|188858 cd09474, LIM2_Lhx2, The second LIM domain of Lhx2

 Score = 80.1 bits (197), Expect = 2e-20
 Identities = 32/50 (64%), Positives = 43/50 (86%)

Query: 1  MGISSSELVMRARDLVFHLHCFTCISCGILLTKGDLFGMRDEMIYCRPHY 50
          +GIS+SE+VMRARDLV+HL+CFTC +C  +LT GD FGM+D ++YCR H+
Sbjct: 10 LGISASEMVMRARDLVYHLNCFTCTTCNKMLTTGDHFGMKDNLVYCRLHF 59

The second LIM domain of Lhx2: Lhx2 belongs to the LHX protein family, which features two tandem N-terminal LIM domains and a C-terminal DNA binding homeodomain. Members of LHX family are found in the nucleus and act as transcription factors or cofactors. LHX proteins are critical for the development of specialized cells in multiple tissue types, including the nervous system, skeletal muscle, the heart, the kidneys, and endocrine organs, such as the pituitary gland and the pancreas. In animals, Lhx2 plays important roles in eye, cerebral cortex, limb, the olfactory organs, and erythrocyte development. Lhx2 gene knockout mice exhibit impaired patterning of the cortical hem and the telencephalon of the developing brain, and a lack of development in olfactory structures. The Lhx2 protein has been shown to bind to the mouse M71 olfactory receptor promoter. Similar to other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein. Length = 59

>gnl|CDD|188859 cd09475, LIM2_Lhx9, The second LIM domain of Lhx9

 Score = 75.1 bits (184), Expect = 2e-18
 Identities = 30/50 (60%), Positives = 40/50 (80%)

Query: 1  MGISSSELVMRARDLVFHLHCFTCISCGILLTKGDLFGMRDEMIYCRPHY 50
          +GIS+SE+VMRAR+ V+HL CFTC +C   LT GD FGM+D ++YCR H+
Sbjct: 10 LGISASEMVMRARESVYHLSCFTCTTCNKTLTTGDHFGMKDNLVYCRAHF 59

The second LIM domain of Lhx9: Lhx9 belongs to the LHX protein family, which features two tandem N-terminal LIM domains and a C-terminal DNA binding homeodomain. Members of LHX family are found in the nucleus and act as transcription factors or cofactors. LHX proteins are critical for the development of specialized cells in multiple tissue types, including the nervous system, skeletal muscle, the heart, the kidneys, and endocrine organs, such as the pituitary gland and the pancreas. Lhx9 is highly homologous to Lhx2. It is expressed in several regions of the developing mouse brain, the spinal cord, the pancreas, in limb mesenchyme, and in the urogenital region. Lhx9 plays critical roles in gonad development. Homozygous mice lacking functional Lhx9 alleles exhibit numerous urogenital defects, such as gonadal agenesis, infertility, and undetectable levels of testosterone and estradiol coupled with high FSH levels. Lhx9 null mice have reduced levels of the Sf1 nuclear receptor that is required for gonadogenesis, and recent studies have shown that Lhx9 is able to activate the Sf1/FtzF1 gene. Lhx9 null mice are phenotypically female, even those that are genotypically male. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein. Length = 59

>gnl|CDD|215907 pfam00412, LIM, LIM domain

 Score = 63.9 bits (156), Expect = 4e-14
 Identities = 22/53 (41%), Positives = 26/53 (49%), Gaps = 1/53 (1%)

Query: 2  GISSSELVMRARDLVFHLHCFTCISCGILLTKGDLFGMRDEMIYCRPHYEILR 54
           I   ELV RA   V+H  CF C  CG  L  GD F  +D  +YC+  Y  L 
Sbjct: 7  PIYDRELVRRALGKVWHPECFRCAVCGKPLGPGDFF-EKDGKLYCKHDYFKLF 58

This family represents two copies of the LIM structural domain. Length = 58

>gnl|CDD|188764 cd09378, LIM2_Lmx1a_Lmx1b, The second LIM domain of Lmx1a and Lmx1b

 Score = 61.3 bits (149), Expect = 3e-13
 Identities = 22/48 (45%), Positives = 30/48 (62%)

Query: 3  ISSSELVMRARDLVFHLHCFTCISCGILLTKGDLFGMRDEMIYCRPHY 50
          I+ SELVMRA + V+HL CF C  C   L KGD F +++  + C+  Y
Sbjct: 8  IAPSELVMRALENVYHLRCFCCCVCERQLQKGDEFVLKEGQLLCKSDY 55

The second LIM domain of Lmx1a and Lmx1b: Lmx1a and Lmx1b belong to the LHX protein family, which features two tandem N-terminal LIM domains and a C-terminal DNA binding homeodomain. Members of LHX family are found in the nucleus and act as transcription factors or cofactors. LHX proteins are critical for the development of specialized cells in multiple tissue types, including the nervous system, skeletal muscle, the heart, the kidneys, and endocrine organs such as the pituitary gland and the pancreas. Mouse Lmx1a is expressed in multiple tissues, including the roof plate of the neural tube, the developing brain, the otic vesicles, the notochord, and the pancreas. In mouse, mutations in Lmx1a result in failure of the roof plate to develop. Lmx1a may act upstream of other roof plate markers such as MafB, Gdf7, Bmp6, and Bmp7. Further characterization of these mice reveals numerous defects including disorganized cerebellum, hippocampus, and cortex; altered pigmentation; female sterility, skeletal defects, and behavioral abnormalities. In the mouse, Lmx1b functions in the developing limbs and eyes, the kidneys, the brain, and in cranial mesenchyme. The disruption of Lmx1b gene results kidney and limb defects. In the brain, Lmx1b is important for generation of mesencephalic dopamine neurons and the differentiation of serotonergic neurons. In the mouse eye, Lmx1b regulates anterior segment (cornea, iris, ciliary body, trabecular meshwork, and lens) development. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein. Length = 55

>gnl|CDD|188765 cd09379, LIM2_AWH, The second LIM domain of Arrowhead (AWH)

 Score = 59.7 bits (145), Expect = 1e-12
 Identities = 21/49 (42%), Positives = 32/49 (65%)

Query: 2  GISSSELVMRARDLVFHLHCFTCISCGILLTKGDLFGMRDEMIYCRPHY 50
           IS+S+ V RARD V+HL CF C +C   L+ G+ F + ++ + C+ HY
Sbjct: 7  NISASDWVRRARDHVYHLACFACDACKRQLSTGEEFALIEDRVLCKAHY 55

The second LIM domain of Arrowhead (AWH): Arrowhead belongs to the LHX protein family, which features two tandem N-terminal LIM domains and a C-terminal DNA binding homeodomain. Members of LHX family are found in the nucleus and act as transcription factors or cofactors. LHX proteins are critical for the development of specialized cells in multiple tissue types, including the nervous system, skeletal muscle, the heart, the kidneys, and endocrine organs such as the pituitary gland and the pancreas. During embryogenesis of Drosophila, Arrowhead is expressed in each abdominal segment and in the labial segment. Late in embryonic development, expression of arrowhead is refined to the abdominal histoblasts and salivary gland imaginal ring cells themselves. The Arrowhead gene required for establishment of a subset of imaginal tissues: the abdominal histoblasts and the salivary gland imaginal rings. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein. Length = 55

>gnl|CDD|200956 pfam00046, Homeobox, Homeobox domain

 Score = 59.4 bits (145), Expect = 1e-12
 Identities = 16/46 (34%), Positives = 30/46 (65%)

Query: 151 KRMRTSFKHHQLRTMKSYFNINQNPDAKDLKQLAQKTGLSKRVLQN 196
           +R RT+F   QL  ++  F  N+ P A++ ++LA+K GL++R ++ 
Sbjct: 1   RRKRTTFTPEQLEELEKEFEKNRYPSAEEREELAKKLGLTERQVKV 46

Length = 57

>gnl|CDD|214528 smart00132, LIM, Zinc-binding domain present in Lin-11, Isl-1, Mec-3

 Score = 59.3 bits (144), Expect = 2e-12
 Identities = 19/48 (39%), Positives = 27/48 (56%), Gaps = 1/48 (2%)

Query: 2  GISSSELVMRARDLVFHLHCFTCISCGILLTKGDLFGMRDEMIYCRPH 49
           I  +E V+RA   V+H  CF C +CG  L+ GD F  +D  +YC+  
Sbjct: 8  PIYGTERVLRALGKVWHPECFKCATCGKPLS-GDTFFEKDGKLYCKDC 54

Zinc-binding domain family. Some LIM domains bind protein partners via tyrosine-containing motifs. LIM domains are found in many key regulators of developmental pathways. Length = 54

>gnl|CDD|197696 smart00389, HOX, Homeodomain

 Score = 58.8 bits (143), Expect = 3e-12
 Identities = 17/47 (36%), Positives = 28/47 (59%)

Query: 150 TKRMRTSFKHHQLRTMKSYFNINQNPDAKDLKQLAQKTGLSKRVLQN 196
            +R RTSF   QL  ++  F  N  P  ++ ++LA+K GLS+R ++ 
Sbjct: 1   KRRKRTSFTPEQLEELEKEFQKNPYPSREEREELAKKLGLSERQVKV 47

DNA-binding factors that are involved in the transcriptional regulation of key developmental processes. Length = 57

>gnl|CDD|188855 cd09471, LIM2_Isl2, The second LIM domain of Isl2

 Score = 58.8 bits (142), Expect = 3e-12
 Identities = 24/47 (51%), Positives = 31/47 (65%)

Query: 1  MGISSSELVMRARDLVFHLHCFTCISCGILLTKGDLFGMRDEMIYCR 47
          +G SSS+LVMRARD V+H+ CF C  C   L  GD F +R+  + CR
Sbjct: 6  LGFSSSDLVMRARDSVYHIECFRCSVCSRQLLPGDEFCLREHELLCR 52

The second LIM domain of Isl2: Isl is a member of LHX protein family, which features two tandem N-terminal LIM domains and a C-terminal DNA binding homeodomain. LHX proteins are critical for the development of specialized cells in multiple tissue types, including the nervous system, skeletal muscle, the heart, the kidneys, and endocrine organs, such as the pituitary gland and the pancreas. Isl proteins are found in the nucleus and act as transcription factors or cofactors. Isl1 and Isl2 are the two conserved members of this family. Mouse Isl2 is expressed in the retinal ganglion cells and the developing spinal cord where it plays a role in motor neuron development. Isl2 may be able to bind to the insulin gene enhancer to promote gene activation. All LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. Length = 55

>gnl|CDD|188761 cd09375, LIM2_Lhx1_Lhx5, The second LIM domain of Lhx1 (also known as Lim1) and Lhx5

 Score = 56.6 bits (137), Expect = 2e-11
 Identities = 23/51 (45%), Positives = 33/51 (64%), Gaps = 1/51 (1%)

Query: 1  MGISSSELVMRARDLVFHLHCFTCISCGILLTKGD-LFGMRDEMIYCRPHY 50
           GIS ++LV RARD VFHL+CFTC+ C   L+ G+ L+ + +    C+  Y
Sbjct: 6  QGISPNDLVRRARDKVFHLNCFTCMVCRKQLSTGEELYILDENKFICKEDY 56

The second LIM domain of Lhx1 (also known as Lim1) and Lhx5. Lhx1 and Lhx5 are closely related members of LHX protein family, which features two tandem N-terminal LIM domains and a C-terminal DNA binding homeodomain. Members of LHX family are found in the nucleus and act as transcription factors or cofactors. LHX proteins are critical for the development of specialized cells in multiple tissue types, including the nervous system, skeletal muscle, the heart, the kidneys, and endocrine organs, such as the pituitary gland and the pancreas. Lhx1 is required for regulating the vertebrate head organizer, the nervous system, and female reproductive tract development. During embryogenesis in the mouse, Lhx1 is expressed early in mesodermal tissue, then later during urogenital, kidney, liver, and nervous system development. In the adult, expression is restricted to the kidney and brain. A mouse embryos with Lhx1 gene knockout cannot grow normal anterior head structures, kidneys, and gonads, but with normally developed trunk and tail morphology. In the developing nervous system, Lhx1 is required to direct the trajectories of motor axons in the limb. Lhx1 null female mice lack the oviducts and uterus. Lhx5 protein may play complementary or overlapping roles with Lhx1. The expression of Lhx5 in the anterior portion of the mouse neural tube suggests a role in patterning of the forebrain. All LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. Length = 56

>gnl|CDD|238039 cd00086, homeodomain, Homeodomain; DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner

 Score = 56.9 bits (138), Expect = 2e-11
 Identities = 14/46 (30%), Positives = 27/46 (58%)

Query: 151 KRMRTSFKHHQLRTMKSYFNINQNPDAKDLKQLAQKTGLSKRVLQN 196
           +R RT F   QL  ++  F  N  P  ++ ++LA++ GL++R ++ 
Sbjct: 1   RRKRTRFTPEQLEELEKEFEKNPYPSREEREELAKELGLTERQVKI 46

Length = 59

>gnl|CDD|188773 cd09387, LIM2_LMO4, The second LIM domain of LMO4 (LIM domain only protein 4)

 Score = 56.0 bits (135), Expect = 3e-11
 Identities = 21/44 (47%), Positives = 28/44 (63%)

Query: 3  ISSSELVMRARDLVFHLHCFTCISCGILLTKGDLFGMRDEMIYC 46
          I +SELVMRA+  V+HL CFTC +C   L  GD F   +  ++C
Sbjct: 8  IPASELVMRAQGNVYHLKCFTCSTCHNQLVPGDRFHYVNGSLFC 51

The second LIM domain of LMO4 (LIM domain only protein 4): LMO4 is a nuclear protein that plays important roles in transcriptional regulation and development. LMO4 is involved in various functions in tumorigenesis and cellular differentiation. LMO4 proteins regulate gene expression by interacting with a wide variety of transcription factors and cofactors to form large transcription complexes. It can interact with Smad proteins, and associate with the promoter of the PAI-1 (plasminogen activator inhibitor-1) gene in a TGFbeta (transforming growth factor beta)-dependent manner. LMO4 can also form a complex with transcription regulator CREB (cAMP response element-binding protein) and interact with CLIM1 and CLIM2. In breast tissue, LMO4 interacts with multiple proteins, including the cofactor CtIP [CtBP (C-terminal binding protein)-interacting protein], the breast and ovarian tumor suppressor BRCA1 (breast-cancer susceptibility gene 1) and the LIM-domain-binding protein LDB1. Functionally, LMO4 is shown to repress BRCA1-mediated transcription activation, thus invoking a potential role for LMO4 as a negative regulator of BRCA1 in sporadic breast cancer. LMO4 also forms complex to both ERa (oestrogen receptor alpha), MTA1 (metastasis tumor antigen 1), and HDACs (histone deacetylases), implying that LMO4 is also a component of the MTA1 corepressor complex. Over-expressed LMO4 represses ERa transactivation functions in an HDAC-dependent manner, and contributes to the process of breast cancer progression by allowing the development of Era-negative phenotypes. All LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. Length = 55

>gnl|CDD|188760 cd09374, LIM2_Isl, The second LIM domain of Isl, a member of LHX protein family

 Score = 55.5 bits (134), Expect = 4e-11
 Identities = 18/46 (39%), Positives = 29/46 (63%)

Query: 2  GISSSELVMRARDLVFHLHCFTCISCGILLTKGDLFGMRDEMIYCR 47
            S ++ VMRAR  ++H+ CF C +C   L  GD F +RD+ ++C+
Sbjct: 7  SFSKNDFVMRARTKIYHIECFRCSACSRQLIPGDEFALRDDGLFCK 52

The second LIM domain of Isl: Isl is a member of LHX protein family, which features two tandem N-terminal LIM domains and a C-terminal DNA binding homeodomain. Isl1 and Isl2 are the two conserved members of this family. Proteins in this group are found in the nucleus and act as transcription factors or cofactors. LHX proteins are critical for the development of specialized cells in multiple tissue types, including the nervous system, skeletal muscle, the heart, the kidneys, and endocrine organs, such as the pituitary gland and the pancreas. Isl-1 is one of the LHX proteins isolated originally by virtue of its ability to bind DNA sequences from the 5'-flanking region of the rat insulin gene in pancreatic insulin-producing cells. Mice deficient in Isl-1 fail to form the dorsal exocrine pancreas and islet cells fail to differentiate. On the other hand, Isl-1 takes part in the pituitary development by activating the gonadotropin-releasing hormone receptor gene together with LHX3 and steroidogenic factor 1. Mouse Isl2 is expressed in the retinal ganglion cells and the developing spinal cord where it plays a role in motor neuron development. Same as Isl1, Isl2 may also be able to bind to the insulin gene enhancer to promote gene activation. All LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. Length = 55

>gnl|CDD|188711 cd08368, LIM, LIM is a small protein-protein interaction domain, containing two zinc fingers

 Score = 55.0 bits (133), Expect = 7e-11
 Identities = 14/42 (33%), Positives = 18/42 (42%), Gaps = 1/42 (2%)

Query: 9  VMRARDLVFHLHCFTCISCGILLTKGDLFGMRDEMIYCRPHY 50
          ++RA    +H  CF C  CG  L     F  +D   YC   Y
Sbjct: 13 LLRALGKKWHPECFKCSVCGKPLGGDS-FYEKDGKPYCEKCY 53

LIM domains are identified in a diverse group of proteins with wide variety of biological functions, including gene expression regulation, cell fate determination, cytoskeleton organization, tumor formation and development. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. They perform their functions through interactions with other protein partners. LIM domains are 50-60 amino acids in size and share two characteristic highly conserved zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. The consensus sequence of LIM domain has been defined as C-x(2)-C-x(16,23)-H-x(2)-[CH]-x(2)-C-x(2)-C-x(16, 21)-C-x(2,3)-[CHD] (where X denotes any amino acid). Length = 53

>gnl|CDD|188856 cd09472, LIM2_Lhx3b, The second LIM domain of Lhx3b

 Score = 51.6 bits (123), Expect = 2e-09
 Identities = 23/51 (45%), Positives = 30/51 (58%), Gaps = 1/51 (1%)

Query: 1  MGISSSELVMRARDLVFHLHCFTCISCGILLTKGDLFG-MRDEMIYCRPHY 50
           GI  +++V RA+D V+HLHCF CI C   L  GD F  M D  + C+  Y
Sbjct: 7  QGIPPTQVVRRAQDFVYHLHCFACIVCKRQLATGDEFYLMEDSRLVCKADY 57

The second LIM domain of Lhx3b. Lhx3b is a member of LHX protein family, which features two tandem N-terminal LIM domains and a C-terminal DNA binding homeodomain. Members of LHX family are found in the nucleus and act as transcription factors or cofactors. LHX proteins are critical for the development of specialized cells in multiple tissue types, including the nervous system, skeletal muscle, the heart, the kidneys, and endocrine organs, such as the pituitary gland and the pancreas. Lhx3b is one of the two isoforms of Lhx3. The Lhx3 gene is expressed in the ventral spinal cord, the pons, the medulla oblongata, and the pineal gland of the developing nervous system during mouse embryogenesis, and transcripts are found in the emergent pituitary gland. Lhx3 functions in concert with other transcription factors to specify interneuron and motor neuron fates during development. Lhx3 proteins have been demonstrated to directly bind to the promoters of several pituitary hormone gene promoters. The Lhx3 gene encodes two isoforms, LHX3a and LHX3b that differ in their amino-terminal sequences, where Lhx3a has longer N-terminal. They show differential activation of pituitary hormone genes and distinct DNA binding properties. In human, Lhx3a trans-activated the alpha-glycoprotein subunit promoter and genes containing a high-affinity Lhx3 binding site more effectively than the hLhx3b isoform. In addition, hLhx3a induce transcription of the TSHbeta-subunit gene by acting on pituitary POU domain factor, Pit-1, while hLhx3b does not. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein. Length = 57

>gnl|CDD|188762 cd09376, LIM2_Lhx3_Lhx4, The second LIM domain of Lhx3-Lhx4 family

 Score = 51.2 bits (123), Expect = 2e-09
 Identities = 21/51 (41%), Positives = 29/51 (56%), Gaps = 1/51 (1%)

Query: 1  MGISSSELVMRARDLVFHLHCFTCISCGILLTKGDLFG-MRDEMIYCRPHY 50
           GI  +++V RA+D V+HL CF C  C   L  GD F  M D+ + C+  Y
Sbjct: 6  EGIPPTQVVRRAQDNVYHLECFACFMCKRQLETGDEFYLMEDDRLVCKKDY 56

The second LIM domain of Lhx3-Lhx4 family: Lhx3 and Lhx4 belong to the LHX protein family, which features two tandem N-terminal LIM domains and a C-terminal DNA binding homeodomain. Members of LHX family are found in the nucleus and act as transcription factors or cofactors. LHX proteins are critical for the development of specialized cells in multiple tissue types, including the nervous system, skeletal muscle, the heart, the kidneys, and endocrine organs, such as the pituitary gland and the pancreas. The LHX3 and LHX4 LIM-homeodomain transcription factors play essential roles in pituitary gland and nervous system development. Although LHX3 and LHX4 share marked sequence homology, the genes have different expression patterns. They play overlapping, but distinct functions during the establishment of the specialized cells of the mammalian pituitary gland and the nervous system. Lhx3 proteins have been demonstrated the ability to directly bind to the promoters/enhancers of several pituitary hormone gene promoters to cause increased transcription.Lhx3a and Lhx3b, whose mRNAs have distinct temporal expression profiles during development, are two isoforms of Lhx3. LHX4 plays essential roles in pituitary gland and nervous system development. In mice, the lhx4 gene is expressed in the developing hindbrain, cerebral cortex, pituitary gland, and spinal cord. LHX4 shows significant sequence similarity to LHX3, particularly to isoforms Lhx3a. In gene regulation experiments, the LHX4 protein exhibits regulation roles towards pituitary genes, acting on their promoters/enhancers. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein. Length = 56

>gnl|CDD|188768 cd09382, LIM2_Lhx6, The second LIM domain of Lhx6

 Score = 50.9 bits (121), Expect = 3e-09
 Identities = 22/48 (45%), Positives = 30/48 (62%)

Query: 3  ISSSELVMRARDLVFHLHCFTCISCGILLTKGDLFGMRDEMIYCRPHY 50
          I +S+ V RAR   +HL CF C SC   L+ G+ FG+ +E + CR HY
Sbjct: 8  IYASDWVRRARGNAYHLACFACFSCKRQLSTGEEFGLVEEKVLCRIHY 55

The second LIM domain of Lhx6. Lhx6 is a member of LHX protein family, which features two tandem N-terminal LIM domains and a C-terminal DNA binding homeodomain. Members of LHX family are found in the nucleus and act as transcription factors or cofactors. LHX proteins are critical for the development of specialized cells in multiple tissue types, including the nervous system, skeletal muscle, the heart, the kidneys, and endocrine organs such as the pituitary gland and the pancreas. Lhx6 functions in brain and nervous system. It is expressed at high levels in several regions of the embryonic mouse CNS, including the telencephalon and hypothalamus, and the first branchial arch. Lhx6 is proposed to have a role in patterning of the mandible and maxilla, and in signaling during odontogenesis. In brain sections, knockdown of Lhx6 gene blocks the normal migration of neurons to the cortex. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. Length = 55

>gnl|CDD|188775 cd09389, LIM2_LMO1_LMO3, The second LIM domain of LMO1 and LMO3 (LIM domain only protein 1 and 3)

 Score = 50.4 bits (120), Expect = 4e-09
 Identities = 21/48 (43%), Positives = 29/48 (60%)

Query: 3  ISSSELVMRARDLVFHLHCFTCISCGILLTKGDLFGMRDEMIYCRPHY 50
          I + E+VMRA+D V+HL CF C  C      GD F +++ MI C+  Y
Sbjct: 8  IPAFEMVMRAKDNVYHLDCFACQLCNQRFCVGDKFFLKNNMILCQMDY 55

The second LIM domain of LMO1 and LMO3 (LIM domain only protein 1 and 3): LMO1 and LMO3 are highly homologous and belong to the LMO protein family. LMO1 and LMO3 are nuclear protein that plays important roles in transcriptional regulation and development. As LIM domains lack intrinsic DNA-binding activity, nuclear LMOs are involved in transcriptional regulation by forming complexes with other transcription factors or cofactors. For example, LMO1 interacts with the the bHLH domain of bHLH transcription factor, TAL1 (T-cell acute leukemia1)/SCL (stem cell leukemia) . LMO1 inhibits the expression of TAL1/SCL target genes. LMO3 facilitates p53 binding to its response elements, which suggests that LMO3 acts as a co-repressor of p53, suppressing p53-dependent transcriptional regulation. In addition, LMO3 interacts with neuronal transcription factor, HEN2, and acts as an oncogene in neuroblastoma. Another binding partner of LMO3 is calcium- and integrin-binding protein CIB, which binds via the second LIM domain (LIM2) of LMO3. One role of the CIB/LMO3 complex is to inhibit cell proliferation. Although LMO1 and LMO3 are highly homologous proteins, they play different roles in the regulation of the pituitary glycoprotein hormone alpha-subunit (alpha GSU) gene. Alpha GSU promoter activity was markedly repressed by LMO1 but activated by LMO3. All LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. Length = 55

>gnl|CDD|188769 cd09383, LIM2_Lhx7_Lhx8, The second LIM domain of Lhx7 and Lhx8

 Score = 49.7 bits (118), Expect = 7e-09
 Identities = 21/48 (43%), Positives = 30/48 (62%)

Query: 3  ISSSELVMRARDLVFHLHCFTCISCGILLTKGDLFGMRDEMIYCRPHY 50
          I S++ V RA+  V+HL CF C SC   L+ G+ F + +E + CR HY
Sbjct: 8  IHSTDWVRRAKGNVYHLACFACFSCKRQLSTGEEFALVEEKVLCRVHY 55

The second LIM domain of Lhx7 and Lhx8: Lhx7 and Lhx8 belong to the LHX protein family, which features two tandem N-terminal LIM domains and a C-terminal DNA binding homeodomain. Members of LHX family are found in the nucleus and act as transcription factors or cofactors. LHX proteins are critical for the development of specialized cells in multiple tissue types, including the nervous system, skeletal muscle, the heart, the kidneys, and endocrine organs such as the pituitary gland and the pancreas. Studies using mutant mice have revealed roles for Lhx7 and Lhx8 in the development of cholinergic neurons in the telencephalon and in basal forebrain development. Mice lacking alleles of the LIM-homeobox gene Lhx7 or Lhx8 display dramatically reduced number of forebrain cholinergic neurons. In addition, Lhx7 mutation affects male and female mice differently, with females appearing more affected than males. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein. Length = 55

>gnl|CDD|188857 cd09473, LIM2_Lhx4, The second LIM domain of Lhx4

 Score = 49.2 bits (117), Expect = 1e-08
 Identities = 22/50 (44%), Positives = 30/50 (60%), Gaps = 1/50 (2%)

Query: 2  GISSSELVMRARDLVFHLHCFTCISCGILLTKGDLFG-MRDEMIYCRPHY 50
          GI  +++V +A+D V+HLHCF CI C   L  GD F  M D  + C+  Y
Sbjct: 7  GIPPTQVVRKAQDFVYHLHCFACIICSRQLATGDEFYLMEDGRLVCKEDY 56

The second LIM domain of Lhx4. Lhx4 belongs to the LHX protein family, which features two tandem N-terminal LIM domains and a C-terminal DNA binding homeodomain. Members of LHX family are found in the nucleus and act as transcription factors or cofactors. LHX proteins are critical for the development of specialized cells in multiple tissue types, including the nervous system, skeletal muscle, the heart, the kidneys, and endocrine organs, such as the pituitary gland and the pancreas. LHX4 plays essential roles in pituitary gland and nervous system development. In mice, the lhx4 gene is expressed in the developing hindbrain, cerebral cortex, pituitary gland, and spinal cord. LHX4 shows significant sequence similarity to LHX3, particularly to isoforms Lhx3a. In gene regulation experiments, the LHX4 protein exhibits regulation roles towards pituitary genes, acting on their promoters/enhancers. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein. Length = 56

>gnl|CDD|188776 cd09390, LIM2_dLMO, The second LIM domain of dLMO (Beaderx)

 Score = 46.8 bits (111), Expect = 1e-07
 Identities = 20/48 (41%), Positives = 25/48 (52%)

Query: 3  ISSSELVMRARDLVFHLHCFTCISCGILLTKGDLFGMRDEMIYCRPHY 50
          I + E+VMRAR  V+HL CF C  C      GD F + +  I C   Y
Sbjct: 8  IPAFEMVMRARTNVYHLECFACQRCNHRFCVGDRFYLCENKILCEYDY 55

The second LIM domain of dLMO (Beaderx): dLMO is a nuclear protein that plays important roles in transcriptional regulation and development. In Drosophila dLMO modulates the activity of LIM-homeodomain protein Apterous (Ap), which regulates the formation of the dorsal-ventral axis of the Drosophila wing. Biochemical analysis shows that dLMO protein influences the activity of Apterous by binding of its cofactor Chip. Further studies shown that dLMO proteins might function in an evolutionarily conserved mechanism involved in patterning the appendages. All LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. Length = 55

>gnl|CDD|188713 cd09327, LIM1_abLIM, The first LIM domain of actin binding LIM (abLIM) proteins

 Score = 41.1 bits (97), Expect = 1e-05
 Identities = 17/42 (40%), Positives = 24/42 (57%), Gaps = 1/42 (2%)

Query: 9  VMRARDLVFHLHCFTCISCGILLTKGDLFGMRDEMIYCRPHY 50
          V+R +D  FH+ CFTC  CG  L +G  F +++   YC   Y
Sbjct: 12 VLRVQDKYFHIKCFTCKVCGCDLAQGGFF-VKEGEYYCTDDY 52

The first LIM domain of actin binding LIM (abLIM) proteins: Three homologous members of the abLIM protein family have been identified; abLIM-1, abLIM-2 and abLIM-3. The N-terminal of abLIM consists of four tandem repeats of LIM domains and the C-terminal of acting binding LIM protein is a villin headpiece domain, which has strong actin binding activity. The abLIM-1, which is expressed in retina, brain, and muscle tissue, has been indicated to function as a tumor suppressor. AbLIM-2 and -3, mainly expressed in muscle and neuronal tissue, bind to F-actin strongly. They may serve as a scaffold for signaling modules of the actin cytoskeleton and thereby modulate transcription. It has shown that LIM domains of abLIMs interact with STARS (striated muscle activator of Rho signaling), which directly binds actin and stimulates serum-response factor (SRF)-dependent transcription. All LIM domains are 50-60 amino acids in size and share two characteristic highly conserved zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. Length = 52

>gnl|CDD|188771 cd09385, LIM2_LMO2, The second LIM domain of LMO2 (LIM domain only protein 2)

 Score = 40.0 bits (93), Expect = 3e-05
 Identities = 16/44 (36%), Positives = 24/44 (54%)

Query: 3  ISSSELVMRARDLVFHLHCFTCISCGILLTKGDLFGMRDEMIYC 46
          I + E+ MR +D V+HL CF C +C      GD + + +  I C
Sbjct: 8  IRAYEMTMRVKDKVYHLECFKCAACQKHFCVGDRYLLINSDIVC 51

The second LIM domain of LMO2 (LIM domain only protein 2): LMO2 is a nuclear protein that plays important roles in transcriptional regulation and development. The two tandem LIM domains of LMO2 support the assembly of a crucial cell-regulatory complex by interacting with both the TAL1-E47 and GATA1 transcription factors to form a DNA-binding complex that is capable of transcriptional activation. LMOs have also been shown to be involved in oncogenesis. LMO1 and LMO2 are activated in T-cell acute lymphoblastic leukemia by distinct chromosomal translocations. LMO2 was also shown to be involved in erythropoiesis and is required for the hematopoiesis in the adult animals. All LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. Length = 56

>gnl|CDD|188736 cd09350, LIM1_TRIP6, The first LIM domain of Thyroid receptor-interacting protein 6 (TRIP6)

 Score = 38.5 bits (90), Expect = 9e-05
 Identities = 17/39 (43%), Positives = 23/39 (58%), Gaps = 1/39 (2%)

Query: 12 ARDLVFHLHCFTCISCGILLTKGDLFGMRDEMIYCRPHY 50
          A D VFH+ CFTC++C   L +G  F   ++  YC P Y
Sbjct: 17 AMDQVFHVDCFTCMTCNGKL-RGQPFYAVEKKAYCEPCY 54

The first LIM domain of Thyroid receptor-interacting protein 6 (TRIP6): TRIP6 is a member of the zyxin LIM protein family and contains three LIM zinc-binding domains at the C-terminal. TRIP6 protein localizes to focal adhesion sites and along actin stress fibers. Recruitment of this protein to the plasma membrane occurs in a lysophosphatidic acid (LPA)-dependent manner. TRIP6 recruits a number of molecules involved in actin assembly, cell motility, survival and transcriptional control. The function of TRIP6 in cell motility is regulated by Src-dependent phosphorylation at a Tyr residue. The phosphorylation activates the coupling to the Crk SH2 domain, which is required for the function of TRIP6 in promoting lysophosphatidic acid (LPA)-induced cell migration. TRIP6 can shuttle to the nucleus to serve as a coactivator of AP-1 and NF-kappaB transcriptional factors. Moreover, TRIP6 can form a ternary complex with the NHERF2 PDZ protein and LPA2 receptor to regulate LPA-induced activation of ERK and AKT, rendering cells resistant to chemotherapy. Recent evidence shows that TRIP6 antagonizes Fas-Induced apoptosis by enhancing the antiapoptotic effect of LPA in cells. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein. Length = 54

>gnl|CDD|188835 cd09451, LIM_RIL, The LIM domain of RIL

 Score = 38.4 bits (89), Expect = 9e-05
 Identities = 16/41 (39%), Positives = 25/41 (60%), Gaps = 1/41 (2%)

Query: 9  VMRARDLVFHLHCFTCISCGILLTKGDLFGMRDEMIYCRPH 49
          +++ARD ++H  CF C  CG+ L +   F + DE +YC  H
Sbjct: 12 IVKARDKLYHPECFMCDDCGLNLKQRGYFFI-DEQLYCETH 51

The LIM domain of RIL: RIL contains an N-terminal PDZ domain, a LIM domain, and a short consensus C-terminal region. It is the smallest molecule in the ALP LIM domain containing protein family. RIL was identified in rat fibroblasts and in human lymphocytes. The LIM domain interacts with the AMPA glutamate receptor in dendritic spines. The consensus C-terminus interacts with PTP-BL, a submembranous protein tyrosine phosphatase and the PDZ domain is responsible to interact with alpha-actinin molecules. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. Length = 53

>gnl|CDD|188751 cd09365, LIM2_LIMK, The second LIM domain of LIMK (LIM domain Kinase )

 Score = 37.7 bits (88), Expect = 2e-04
 Identities = 17/53 (32%), Positives = 23/53 (43%), Gaps = 12/53 (22%)

Query: 8  LVMRARDLVFHLHCFTCISCGILLTKGDLFGMRDEMIYCRPHYEILRHRDYCG 60
           VM A D  FH  CF+C SC   +  GD + +            + R + YCG
Sbjct: 11 PVMVAGDHKFHPECFSCSSCKAFIGDGDSYAL------------VERSKLYCG 51

The second LIM domain of LIMK (LIM domain Kinase ): LIMK protein family is comprised of two members LIMK1 and LIMK2. LIMK contains two LIM domains, a PDZ domain and a kinase domain. LIMK is involved in the regulation of actin polymerization and microtubule disassembly. LIMK influences architecture of the actin cytoskeleton by regulating the activity of the cofilin family proteins cofilin1, cofilin2, and destrin. The mechanism of the activation is to phosphorylates cofilin on serine 3 and inactivates its actin-severing activity, and altering the rate of actin depolymerization. LIMKs can function in both cytoplasm and nucleus and are expressed in all tissues. Both LIMK1 and LIMK2 can act in the nucleus to suppress Rac/Cdc42-dependent cyclin D1 expression. However, LIMK1 and LIMk2 have different cellular locations. While LIMK1 localizes mainly at focal adhesions, LIMK2 is found in cytoplasmic punctae, suggesting that they may have different cellular functions. The LIM domains of LIMK have been shown to play an important role in regulating kinase activity and likely also contribute to LIMK function by acting as sites of protein-to-protein interactions. All LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. Length = 54

>gnl|CDD|188744 cd09358, LIM_Mical_like, The LIM domain of Mical (molecule interacting with CasL) like family

 Score = 36.5 bits (85), Expect = 5e-04
 Identities = 12/35 (34%), Positives = 19/35 (54%), Gaps = 1/35 (2%)

Query: 16 VFHLHCFTCISCGILLTKGDLFGMRDEMIYCRPHY 50
          +FH  CF C  C   L  G+   +  + +YC+PH+
Sbjct: 20 LFHKSCFRCSHCNKTLRLGNYASLEGK-LYCKPHF 53

The LIM domain of Mical (molecule interacting with CasL) like family: Known members of this family includes LIM domain containing proteins; Mical (molecule interacting with CasL), pollen specific protein SF3, Eplin, xin actin-binding repeat-containing protein 2 (XIRP2) and Ltd-1. The members of this family function mainly at the cytoskeleton and focal adhesions. They interact with transcription factors or other signaling molecules to play roles in muscle development, neuronal differentiation, cell growth and mobility. Eplin has also found to be tumor suppressor. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs.. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein. Length = 53

>gnl|CDD|188848 cd09464, LIM2_LIMK1, The second LIM domain of LIMK1 (LIM domain Kinase 1)

 Score = 36.4 bits (84), Expect = 6e-04
 Identities = 14/43 (32%), Positives = 25/43 (58%), Gaps = 1/43 (2%)

Query: 5  SSELVMRARDLVFHLHCFTCISCGILLTKGDLFGMRDEM-IYC 46
          ++ LVM A +  +H  CF+C+ CG  +  GD + + +   +YC
Sbjct: 9  TTGLVMVAGEQKYHPECFSCLRCGAFIGDGDTYALVEHSKLYC 51

The second LIM domain of LIMK1 (LIM domain Kinase 1): LIMK1 belongs to the LIMK protein family, which comprises LIMK1 and LIMK2. LIMK contains two LIM domains, a PDZ domain, and a kinase domain. LIMK is involved in the regulation of actin polymerization and microtubule disassembly. LIMK influences architecture of the actin cytoskeleton by regulating the activity of the cofilin family proteins cofilin1, cofilin2, and destrin. The mechanism of the activation is to phosphorylates cofilin on serine 3 and inactivates its actin-severing activity, and altering the rate of actin depolymerization. LIMKs can function in both cytoplasm and nucleus. Both LIMK1 and LIMK2 can act in the nucleus to suppress Rac/Cdc42-dependent cyclin D1 expression. LIMK1 is expressed in all tissues and is localized to focal adhesions in the cell. LIMK1 can form homodimers upon binding of HSP90 and is activated by Rho effector Rho kinase and MAPKAPK2. LIMK1 is important for normal central nervous system development, and its deletion has been implicated in the development of the human genetic disorder Williams syndrome. Moreover, LIMK1 up-regulates the promoter activity of urokinase type plasminogen activator and induces its mRNA and protein expression in breast cancer cells. The LIM domains have been shown to play an important role in regulating kinase activity and likely also contribute to LIMK function by acting as sites of protein-to-protein interactions. All LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. Length = 55

>gnl|CDD|188752 cd09366, LIM1_Isl, The first LIM domain of Isl, a member of LHX protein family

 Score = 35.8 bits (83), Expect = 0.001
 Identities = 14/39 (35%), Positives = 18/39 (46%)

Query: 12 ARDLVFHLHCFTCISCGILLTKGDLFGMRDEMIYCRPHY 50
          A DL +H  C  C  CG  L +     +RD   YC+  Y
Sbjct: 17 APDLEWHAACLKCAECGQYLDETCTCFVRDGKTYCKRDY 55

The first LIM domain of Isl: Isl is a member of LHX protein family, which features two tandem N-terminal LIM domains and a C-terminal DNA binding homeodomain. Isl1 and Isl2 are the two conserved members of this family. Proteins in this group are found in the nucleus and act as transcription factors or cofactors. LHX proteins are critical for the development of specialized cells in multiple tissue types, including the nervous system, skeletal muscle, the heart, the kidneys, and endocrine organs, such as the pituitary gland and the pancreas. Isl-1 is one of the LHX proteins isolated originally by virtue of its ability to bind DNA sequences from the 5'-flanking region of the rat insulin gene in pancreatic insulin-producing cells. Mice deficient in Isl-1 fail to form the dorsal exocrine pancreas and islet cells fail to differentiate. On the other hand, Isl-1 takes part in the pituitary development by activating the gonadotropin-releasing hormone receptor gene together with LHX3 and steroidogenic factor 1. Mouse Is l2 is expressed in the retinal ganglion cells and the developing spinal cord where it plays a role in motor neuron development. Same as Isl1, Isl2 may also be able to bind to the insulin gene enhancer to promote gene activation. All LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. Length = 55

>gnl|CDD|188870 cd09486, LIM_Eplin_like_1, a LIM domain subfamily on a group of proteins with unknown function

 Score = 35.3 bits (81), Expect = 0.001
 Identities = 16/39 (41%), Positives = 20/39 (51%), Gaps = 1/39 (2%)

Query: 12 ARDLVFHLHCFTCISCGILLTKGDLFGMRDEMIYCRPHY 50
          A  LVFH  CF C  C   L+ G    +  E  YC+PH+
Sbjct: 16 ADKLVFHNSCFCCKHCNAKLSLGSYAALHGEF-YCKPHF 53

This model represents a LIM domain subfamily of Eplin-like family. This family shows highest homology to the LIM domains on Eplin and XIRP2 protein families. Epithelial Protein Lost in Neoplasm is a cytoskeleton-associated tumor suppressor whose expression inversely correlates with cell growth, motility, invasion and cancer mortality. Xirp2 is expressed in muscles and is an important effector of the Ang II signaling pathway in the heart. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein. Length = 53

>gnl|CDD|188748 cd09362, LIM2_Enigma_like, The second LIM domain of Enigma-like family

 Score = 35.5 bits (82), Expect = 0.001
 Identities = 15/42 (35%), Positives = 19/42 (45%), Gaps = 1/42 (2%)

Query: 9  VMRARDLVFHLHCFTCISCGILLTKGDLFGMRDEMIYCRPHY 50
          VM A    +H+ CF C +C   +    LF M D   YC   Y
Sbjct: 12 VMHALKQTWHVSCFVCAACKQPI-GNSLFHMEDGEPYCEKDY 52

The second LIM domain of Enigma-like family: The Enigma LIM domain family is comprised of three members: Enigma, ENH, and Cypher (mouse)/ZASP (human). These subfamily members contain a single PDZ domain at the N-terminus and three LIM domains at the C-terminus. Enigma was initially characterized in humans and is expressed in multiple tissues, such as skeletal muscle, heart, bone and brain. The third LIM domain specifically interacts with the insulin receptor and the second LIM domain interacts with the receptor tyrosine kinase Ret and the adaptor protein APS. Thus Enigma is implicated in signal transduction processes, such as mitogenic activity, insulin related actin organization, and glucose metabolism. The second member, ENH protein, was first identified in rat brain. It has been shown that ENH interacts with protein kinase D1 (PKD1) via its LIM domains and forms a complex with PKD1 and the alpha1C subunit of cardiac L-type voltage-gated calcium channel in rat neonatal cardiomyocytes. The N-terminal PDZ domain interacts with alpha-actinin at the Z-line. ZASP/Cypher is required for maintenance of Z-line structure during muscle contraction, but not required for Z-line assembly. In heart, Cypher/ZASP plays a structural role through its interaction with cytoskeletal Z-line proteins. In addition, there is increasing evidence that Cypher/ZASP also performs signaling functions. Studies reveal that Cypher/ZASP interacts with and directs PKC to the Z-line, where PKC phosphorylates downstream signaling targets. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. Length = 52

>gnl|CDD|188798 cd09414, LIM1_LIMPETin, The first LIM domain of protein LIMPETin

 Score = 35.5 bits (82), Expect = 0.001
 Identities = 16/38 (42%), Positives = 22/38 (57%), Gaps = 3/38 (7%)

Query: 14 DLVFHLHCFTCISCGILLTKGDL-FGMRDEMIYCRPHY 50
           L++H  CF C +C  LL   DL + + D+ IYC  HY
Sbjct: 23 SLLWHPACFRCSTCEELLV--DLTYCVHDDQIYCERHY 58

The first LIM domain of protein LIMPETin: LIMPETin contains 6 LIM domains at the C-terminal and an N-terminal PET domain. Four of the six LIM domains are highly homologous to the four and half LIM domain protein family and two of them show sequence similarity to the LIM domains of the Testin family. Thus, LIMPETin may be the recombinant product of genes coding testin and FHL proteins. In Schistosoma mansoni, where LIMPETin was first identified, LIMPETin is down regulated in sexually mature adult Schistosoma females compared to sexually immature adult females and adult male. Its differential expression indicates that it is a transcription regulator. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. Length = 58

>gnl|CDD|188778 cd09392, LIM2_Lrg1p_like, The second LIM domain of Lrg1p, a LIM and RhoGap domain containing protein

 Score = 34.3 bits (79), Expect = 0.004
 Identities = 11/34 (32%), Positives = 16/34 (47%)

Query: 17 FHLHCFTCISCGILLTKGDLFGMRDEMIYCRPHY 50
          +H+  FTC  C  +    D +   +  IYC  HY
Sbjct: 20 YHVEHFTCSVCPTVFGPNDSYYEHEGKIYCHYHY 53

The second LIM domain of Lrg1p, a LIM and RhoGap domain containing protein: The members of this family contain three tandem repeats of LIM domains and a Rho-type GTPase activating protein (RhoGap) domain. Lrg1p is a Rho1 GTPase-activating protein required for efficient cell fusion in yeast. Lrg1p-GAP domain strongly and specifically stimulates the GTPase activity of Rho1p, a regulator of beta (1-3)-glucan synthase in vitro. The LIM domain is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein. Length = 53

>gnl|CDD|188746 cd09360, LIM_ALP_like, The LIM domain of ALP (actinin-associated LIM protein) family

 Score = 33.9 bits (78), Expect = 0.004
 Identities = 17/41 (41%), Positives = 22/41 (53%), Gaps = 1/41 (2%)

Query: 9  VMRARDLVFHLHCFTCISCGILLTKGDLFGMRDEMIYCRPH 49
          V++ARD   H  CF C  CG+ L     F + DE +YC  H
Sbjct: 12 VVKARDKNRHPECFVCADCGLNLKNKGYFFIEDE-LYCETH 51

This family represents the LIM domain of ALP (actinin-associated LIM protein) family. Four proteins: ALP, CLP36, RIL, and Mystique have been classified into the ALP subfamily of LIM domain proteins. Each member of the subfamily contains an N-terminal PDZ domain and a C-terminal LIM domain. Functionally, these proteins bind to alpha-actinin through their PDZ domains and bind or other signaling molecules through their LIM domains. ALP proteins have been implicated in cardiac and skeletal muscle structure, function and disease, platelet, and epithelial cell motility. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. Length = 52

>gnl|CDD|188712 cd09326, LIM_CRP_like, The LIM domains of Cysteine Rich Protein (CRP) family

 Score = 33.7 bits (78), Expect = 0.004
 Identities = 13/34 (38%), Positives = 15/34 (44%), Gaps = 1/34 (2%)

Query: 17 FHLHCFTCISCGILLTKGDLFGMRDEMIYCRPHY 50
          +H  CFTC  C   L    L    D  IYC+  Y
Sbjct: 21 WHKSCFTCAVCNKRLDSTTL-AEHDGEIYCKSCY 53

The LIM domains of Cysteine Rich Protein (CRP) family: Cysteine-rich proteins (CRPs) are characterized by the presence of two LIM domains linked to a short glycine-rich repeats (GRRs). The known CRP family members include CRP1, CRP2, and CRP3/MLP. CRP1, CRP2 and CRP3 share a conserved nuclear targeting signal (K/R-K/R-Y-G-P-K), which supports the fact that these proteins function not only in the cytoplasm but also in the nucleus. CRPs control regulatory pathways during cellular differentiation, and involve in complex transcription control, and the organization as well as the arrangement of the myofibrillar/cytoskeletal network. CRP1, CRP2, and CRP3/MLP are involved in promoting protein assembly along the actin-based cytoskeleton. All LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. Length = 53

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	196
KOG4577|consensus	383		99.82
KOG0484|consensus	125		99.21
TIGR01565	58	homeo_ZF_HD homeobox domain, ZF-HD class. This mod	99.05
KOG2251|consensus	228		99.0
KOG0490|consensus	235		98.96
PF00412	58	LIM: LIM domain; InterPro: IPR001781 Zinc finger (	98.94
KOG0850|consensus	245		98.9
KOG0488|consensus	309		98.85
KOG0843|consensus	197		98.81
KOG0489|consensus	261		98.78
KOG0485|consensus	268		98.78
KOG0494|consensus	332		98.75
KOG0842|consensus	307		98.74
KOG1701|consensus	468		98.73
KOG0486|consensus	351		98.73
PF00046	57	Homeobox: Homeobox domain not present here.; Inter	98.72
KOG1701|consensus	468		98.59
smart00389	56	HOX Homeodomain. DNA-binding factors that are invo	98.57
KOG0493|consensus	342		98.51
cd00086	59	homeodomain Homeodomain; DNA binding domains invol	98.42
KOG0492|consensus	246		98.35
KOG0490|consensus	235		98.32
KOG0487|consensus	308		98.27
KOG2272|consensus	332		98.22
KOG0848|consensus	317		98.13
KOG0491|consensus	194		98.1
KOG4577|consensus	383		98.07
KOG0849|consensus	354		97.97
KOG0844|consensus	408		97.92
KOG2272|consensus	332		97.87
COG5576	156	Homeodomain-containing transcription factor [Trans	97.64
KOG1703|consensus	479		97.63
KOG3802|consensus	398		97.62
KOG1044|consensus	670		97.45
KOG2252|consensus	558		97.32
smart00132	39	LIM Zinc-binding domain present in Lin-11, Isl-1,	97.29
KOG1044|consensus	670		96.89
KOG1702|consensus	264		96.81
KOG1168|consensus	385		96.32
KOG1700|consensus	200		96.32
KOG0483|consensus	198		96.29
KOG0847|consensus	288		96.07
PF05920	40	Homeobox_KN: Homeobox KN domain; InterPro: IPR0084	95.66
KOG1700|consensus	200		95.27
KOG0775|consensus	304		93.68
KOG0774|consensus	334		91.84
KOG1146|consensus	1406		89.32
KOG1703|consensus	479		87.75
PF04967	53	HTH_10: HTH DNA binding domain; InterPro: IPR00705	84.38

>KOG4577|consensus

Probab=99.82  E-value=8e-21  Score=157.29  Aligned_cols=112  Identities=36%  Similarity=0.670  Sum_probs=95.8

Q ss_pred             CCCChHHHHHHHHhHHHhhhhhhhhhhcceeccCCcccc-ccceeeeccchhhhhhccccCcccccCCCCCCCCCCCCcc
Q psy17504          1 MGISSSELVMRARDLVFHLHCFTCISCGILLTKGDLFGM-RDEMIYCRPHYEILRHRDYCGSAEIEQPMSPRPAPWQPTT   79 (196)
Q Consensus         1 ~~i~~~~~v~~a~~~~~H~~CF~C~~C~~~L~~G~~f~~-~~~~~~C~~~y~~~~~~~~~~~~~~~~~~~p~~~~~~~~~   79 (196)
                      +||.|+..|.+|.+.+||+.||.|++|+++|.+|++|++ .++++.|+.||+....-..                     
T Consensus       100 ~GIpPtqVVRkAqd~VYHl~CF~C~iC~R~L~TGdEFYLmeD~rLvCK~DYE~Ak~k~~---------------------  158 (383)
T KOG4577|consen  100 EGIPPTQVVRKAQDFVYHLHCFACFICKRQLATGDEFYLMEDARLVCKDDYETAKQKHC---------------------  158 (383)
T ss_pred             CCCChHHHHHHhhcceeehhhhhhHhhhcccccCCeeEEeccceeehhhhHHHHHhccc---------------------
Confidence            589999999999999999999999999999999999965 6789999999986532100                     


Q ss_pred             cccCCcccccccccCCCCCccccccceeeccccchhhhccCCccccccccccccCCCCCCCCCccccccccchhhcccch
Q psy17504         80 VQKGRPRKRKLSVDSPTPPSEDINANVMRIPSTTLEMLHSGDLSSSMESLSYESGAGNSSPGSGVHSHQRTKRMRTSFKH  159 (196)
Q Consensus        80 ~~~g~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~gs~~~~~~k~rR~RT~ft~  159 (196)
                                                      .                 .+++  +           ...||+||++|+
T Consensus       159 --------------------------------~-----------------~l~g--d-----------~~nKRPRTTItA  176 (383)
T KOG4577|consen  159 --------------------------------N-----------------ELEG--D-----------ASNKRPRTTITA  176 (383)
T ss_pred             --------------------------------c-----------------cccc--c-----------cccCCCcceeeH
Confidence                                            0                 0111  0           124789999999


Q ss_pred             hhHhhhhhhhcccCCCChHHHHHHHHHhCcchhhhc
Q psy17504        160 HQLRTMKSYFNINQNPDAKDLKQLAQKTGLSKRVLQ  195 (196)
Q Consensus       160 ~Ql~~L~~~F~~~~~p~~~~r~~La~~lgL~~~~Vq  195 (196)
                      .||+.|+.+|...+.|.++.||+|+..+||..++||
T Consensus       177 KqLETLK~AYn~SpKPARHVREQLsseTGLDMRVVQ  212 (383)
T KOG4577|consen  177 KQLETLKQAYNTSPKPARHVREQLSSETGLDMRVVQ  212 (383)
T ss_pred             HHHHHHHHHhcCCCchhHHHHHHhhhccCcceeehh
Confidence            999999999999999999999999999999999997

>KOG0484|consensus

Probab=99.21  E-value=5e-12  Score=90.54  Aligned_cols=49  Identities=27%  Similarity=0.483  Sum_probs=47.0

Q ss_pred             ccccchhhcccchhhHhhhhhhhcccCCCChHHHHHHHHHhCcchhhhc
Q psy17504        147 HQRTKRMRTSFKHHQLRTMKSYFNINQNPDAKDLKQLAQKTGLSKRVLQ  195 (196)
Q Consensus       147 ~~k~rR~RT~ft~~Ql~~L~~~F~~~~~p~~~~r~~La~~lgL~~~~Vq  195 (196)
                      ++|.||.||+||..||.+||+.|...||||+..|++||.++.|++..||
T Consensus        14 krKQRRIRTTFTS~QLkELErvF~ETHYPDIYTREEiA~kidLTEARVQ   62 (125)
T KOG0484|consen   14 KRKQRRIRTTFTSAQLKELERVFAETHYPDIYTREEIALKIDLTEARVQ   62 (125)
T ss_pred             HHHhhhhhhhhhHHHHHHHHHHHHhhcCCcchhHHHHHHhhhhhHHHHH
Confidence            4678999999999999999999999999999999999999999999987

>TIGR01565 homeo_ZF_HD homeobox domain, ZF-HD class

Probab=99.05  E-value=1.4e-10  Score=75.56  Aligned_cols=45  Identities=20%  Similarity=0.434  Sum_probs=43.8

Q ss_pred             chhhcccchhhHhhhhhhhcccCC----CChHHHHHHHHHhCcchhhhc
Q psy17504        151 KRMRTSFKHHQLRTMKSYFNINQN----PDAKDLKQLAQKTGLSKRVLQ  195 (196)
Q Consensus       151 rR~RT~ft~~Ql~~L~~~F~~~~~----p~~~~r~~La~~lgL~~~~Vq  195 (196)
                      ||.||.||.+|+..|+..|+.++|    |+..++++||..|||++++||
T Consensus         2 kR~RT~Ft~~Q~~~Le~~fe~~~y~~~~~~~~~r~~la~~lgl~~~vvK   50 (58)
T TIGR01565         2 KRRRTKFTAEQKEKMRDFAEKLGWKLKDKRREEVREFCEEIGVTRKVFK   50 (58)
T ss_pred             CCCCCCCCHHHHHHHHHHHHHcCCCCCCCCHHHHHHHHHHhCCCHHHee
Confidence            789999999999999999999999    999999999999999999987

This model represents a class of homoebox domain that differs substantially from the typical homoebox domain described in pfam model pfam00046. It is found in both C4 and C3 plants.

>KOG2251|consensus

Probab=99.00  E-value=2.1e-10  Score=92.56  Aligned_cols=51  Identities=29%  Similarity=0.420  Sum_probs=48.3

Q ss_pred             cccccchhhcccchhhHhhhhhhhcccCCCChHHHHHHHHHhCcchhhhcC
Q psy17504        146 SHQRTKRMRTSFKHHQLRTMKSYFNINQNPDAKDLKQLAQKTGLSKRVLQN  196 (196)
Q Consensus       146 ~~~k~rR~RT~ft~~Ql~~L~~~F~~~~~p~~~~r~~La~~lgL~~~~Vq~  196 (196)
                      ..+|.||.||+||..||++||..|.+.+|||..+||+||.+|+|++.+||.
T Consensus        33 ~pRkqRRERTtFtr~QlevLe~LF~kTqYPDv~~rEelAlklnLpeSrVqV   83 (228)
T KOG2251|consen   33 GPRKQRRERTTFTRKQLEVLEALFAKTQYPDVFMREELALKLNLPESRVQV   83 (228)
T ss_pred             cchhcccccceecHHHHHHHHHHHHhhcCccHHHHHHHHHHhCCchhhhhh
Confidence            457889999999999999999999999999999999999999999999983

>KOG0490|consensus

Probab=98.96  E-value=5e-10  Score=91.59  Aligned_cols=47  Identities=19%  Similarity=0.076  Sum_probs=45.0

Q ss_pred             ccchhhcccchhhHhhhhhhhcccCCCChHHHHHHHHHhCcchhhhc
Q psy17504        149 RTKRMRTSFKHHQLRTMKSYFNINQNPDAKDLKQLAQKTGLSKRVLQ  195 (196)
Q Consensus       149 k~rR~RT~ft~~Ql~~L~~~F~~~~~p~~~~r~~La~~lgL~~~~Vq  195 (196)
                      +.||.||.|+..|+.+|+++|+++|||+...|+.||..+++++..||
T Consensus        59 ~~rr~rt~~~~~ql~~ler~f~~~h~Pd~~~r~~la~~~~~~e~rVq  105 (235)
T KOG0490|consen   59 SKRCARCKFTISQLDELERAFEKVHLPCFACRECLALLLTGDEFRVQ  105 (235)
T ss_pred             cccccCCCCCcCHHHHHHHhhcCCCcCccchHHHHhhcCCCCeeeee
Confidence            56889999999999999999999999999999999999999999987

>PF00412 LIM: LIM domain; InterPro: IPR001781 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule

Probab=98.94  E-value=1.3e-11  Score=80.03  Aligned_cols=51  Identities=35%  Similarity=0.716  Sum_probs=42.9

Q ss_pred             CChHHHHHHHHhHHHhhhhhhhhhhcceeccCCccccccceeeeccchhhhh
Q psy17504          3 ISSSELVMRARDLVFHLHCFTCISCGILLTKGDLFGMRDEMIYCRPHYEILR   54 (196)
Q Consensus         3 i~~~~~v~~a~~~~~H~~CF~C~~C~~~L~~G~~f~~~~~~~~C~~~y~~~~   54 (196)
                      |.+.+.++++.++.||..||+|..|++.|..+. |.+.++++||+.||..+|
T Consensus         8 I~~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~-~~~~~~~~~C~~c~~~~f   58 (58)
T PF00412_consen    8 IYGTEIVIKAMGKFWHPECFKCSKCGKPLNDGD-FYEKDGKPYCKDCYQKRF   58 (58)
T ss_dssp             ESSSSEEEEETTEEEETTTSBETTTTCBTTTSS-EEEETTEEEEHHHHHHHT
T ss_pred             ccCcEEEEEeCCcEEEccccccCCCCCccCCCe-eEeECCEEECHHHHhhhC
Confidence            445556667899999999999999999996555 888899999999998764

Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents LIM-type zinc finger (Znf) domains. LIM domains coordinate one or more zinc atoms, and are named after the three proteins (LIN-11, Isl1 and MEC-3) in which they were first found. They consist of two zinc-binding motifs that resemble GATA-like Znf's, however the residues holding the zinc atom(s) are variable, involving Cys, His, Asp or Glu residues. LIM domains are involved in proteins with differing functions, including gene expression, and cytoskeleton organisation and development [, ]. Protein containing LIM Znf domains include: Caenorhabditis elegans mec-3; a protein required for the differentiation of the set of six touch receptor neurons in this nematode. C. elegans. lin-11; a protein required for the asymmetric division of vulval blast cells. Vertebrate insulin gene enhancer binding protein isl-1. Isl-1 binds to one of the two cis-acting protein-binding domains of the insulin gene. Vertebrate homeobox proteins lim-1, lim-2 (lim-5) and lim3. Vertebrate lmx-1, which acts as a transcriptional activator by binding to the FLAT element; a beta-cell-specific transcriptional enhancer found in the insulin gene. Mammalian LH-2, a transcriptional regulatory protein involved in the control of cell differentiation in developing lymphoid and neural cell types. Drosophila melanogaster (Fruit fly) protein apterous, required for the normal development of the wing and halter imaginal discs. Vertebrate protein kinases LIMK-1 and LIMK-2. Mammalian rhombotins. Rhombotin 1 (RBTN1 or TTG-1) and rhombotin-2 (RBTN2 or TTG-2) are proteins of about 160 amino acids whose genes are disrupted by chromosomal translocations in T-cell leukemia. Mammalian and avian cysteine-rich protein (CRP), a 192 amino-acid protein of unknown function. Seems to interact with zyxin. Mammalian cysteine-rich intestinal protein (CRIP), a small protein which seems to have a role in zinc absorption and may function as an intracellular zinc transport protein. Vertebrate paxillin, a cytoskeletal focal adhesion protein. Mus musculus (Mouse) testin which should not be confused with rat testin which is a thiol protease homologue (see IPR000169 from INTERPRO). Helianthus annuus (Common sunflower) pollen specific protein SF3. Chicken zyxin. Zyxin is a low-abundance adhesion plaque protein which has been shown to interact with CRP. Yeast protein LRG1 which is involved in sporulation []. Saccharomyces cerevisiae (Baker's yeast) rho-type GTPase activating protein RGA1/DBM1. C. elegans homeobox protein ceh-14. C. elegans homeobox protein unc-97. S. cerevisiae hypothetical protein YKR090w. C. elegans hypothetical proteins C28H8.6. These proteins generally contain two tandem copies of the LIM domain in their N-terminal section. Zyxin and paxillin are exceptions in that they contain respectively three and four LIM domains at their C-terminal extremity. In apterous, isl-1, LH-2, lin-11, lim-1 to lim-3, lmx-1 and ceh-14 and mec-3 there is a homeobox domain some 50 to 95 amino acids after the LIM domains. LIM domains contain seven conserved cysteine residues and a histidine. The arrangement followed by these conserved residues is: C-x(2)-C-x(16,23)-H-x(2)-[CH]-x(2)-C-x(2)-C-x(16,21)-C-x(2,3)-[CHD] LIM domains bind two zinc ions []. LIM does not bind DNA, rather it seems to act as an interface for protein-protein interaction. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2CO8_A 2EGQ_A 2CUR_A 3IXE_B 1CTL_A 1B8T_A 1X62_A 2DFY_C 1IML_A 2CUQ_A ....

>KOG0850|consensus

Probab=98.90  E-value=7e-10  Score=89.95  Aligned_cols=52  Identities=19%  Similarity=0.299  Sum_probs=49.7

Q ss_pred             cccccccchhhcccchhhHhhhhhhhcccCCCChHHHHHHHHHhCcchhhhc
Q psy17504        144 VHSHQRTKRMRTSFKHHQLRTMKSYFNINQNPDAKDLKQLAQKTGLSKRVLQ  195 (196)
Q Consensus       144 ~~~~~k~rR~RT~ft~~Ql~~L~~~F~~~~~p~~~~r~~La~~lgL~~~~Vq  195 (196)
                      +++.||.|+.||+|+..||..|.+.|++.+|+-..+|.+||..|||+..|||
T Consensus       116 Ngk~KK~RKPRTIYSS~QLqaL~rRFQkTQYLALPERAeLAAsLGLTQTQVK  167 (245)
T KOG0850|consen  116 NGKGKKVRKPRTIYSSLQLQALNRRFQQTQYLALPERAELAASLGLTQTQVK  167 (245)
T ss_pred             CCCcccccCCcccccHHHHHHHHHHHhhcchhcCcHHHHHHHHhCCchhHhh
Confidence            4578899999999999999999999999999999999999999999999997

>KOG0488|consensus

Probab=98.85  E-value=1.9e-09  Score=92.51  Aligned_cols=50  Identities=24%  Similarity=0.410  Sum_probs=47.6

Q ss_pred             cccccchhhcccchhhHhhhhhhhcccCCCChHHHHHHHHHhCcchhhhc
Q psy17504        146 SHQRTKRMRTSFKHHQLRTMKSYFNINQNPDAKDLKQLAQKTGLSKRVLQ  195 (196)
Q Consensus       146 ~~~k~rR~RT~ft~~Ql~~L~~~F~~~~~p~~~~r~~La~~lgL~~~~Vq  195 (196)
                      ..||+|+.||+||..||.+||..|+++.|++..+|.+||++|||+..|||
T Consensus       168 ~pkK~RksRTaFT~~Ql~~LEkrF~~QKYLS~~DR~~LA~~LgLTdaQVK  217 (309)
T KOG0488|consen  168 TPKKRRKSRTAFSDHQLFELEKRFEKQKYLSVADRIELAASLGLTDAQVK  217 (309)
T ss_pred             CCcccccchhhhhHHHHHHHHHHHHHhhcccHHHHHHHHHHcCCchhhHH
Confidence            44788889999999999999999999999999999999999999999997

>KOG0843|consensus

Probab=98.81  E-value=2.4e-09  Score=83.93  Aligned_cols=48  Identities=38%  Similarity=0.436  Sum_probs=46.3

Q ss_pred             cccchhhcccchhhHhhhhhhhcccCCCChHHHHHHHHHhCcchhhhc
Q psy17504        148 QRTKRMRTSFKHHQLRTMKSYFNINQNPDAKDLKQLAQKTGLSKRVLQ  195 (196)
Q Consensus       148 ~k~rR~RT~ft~~Ql~~L~~~F~~~~~p~~~~r~~La~~lgL~~~~Vq  195 (196)
                      .|.||.||+||.+||..||.+|+.++|....+|++||+.|+|++.|||
T Consensus       100 ~~~kr~RT~ft~~Ql~~LE~~F~~~~Yvvg~eR~~LA~~L~LsetQVk  147 (197)
T KOG0843|consen  100 MRPKRIRTAFTPEQLLKLEHAFEGNQYVVGAERKQLAQSLSLSETQVK  147 (197)
T ss_pred             cCCCccccccCHHHHHHHHHHHhcCCeeechHHHHHHHHcCCChhHhh
Confidence            378999999999999999999999999999999999999999999997

>KOG0489|consensus

Probab=98.78  E-value=3.2e-09  Score=89.29  Aligned_cols=48  Identities=25%  Similarity=0.388  Sum_probs=46.2

Q ss_pred             cccchhhcccchhhHhhhhhhhcccCCCChHHHHHHHHHhCcchhhhc
Q psy17504        148 QRTKRMRTSFKHHQLRTMKSYFNINQNPDAKDLKQLAQKTGLSKRVLQ  195 (196)
Q Consensus       148 ~k~rR~RT~ft~~Ql~~L~~~F~~~~~p~~~~r~~La~~lgL~~~~Vq  195 (196)
                      .+.||.||.||..||.+||..|+.|+|+++..|.+||..|.|+|+|||
T Consensus       157 ~~~kR~RtayT~~QllELEkEFhfN~YLtR~RRiEiA~~L~LtErQIK  204 (261)
T KOG0489|consen  157 GKSKRRRTAFTRYQLLELEKEFHFNKYLTRSRRIEIAHALNLTERQIK  204 (261)
T ss_pred             CCCCCCCcccchhhhhhhhhhhccccccchHHHHHHHhhcchhHHHHH
Confidence            467899999999999999999999999999999999999999999997

>KOG0485|consensus

Probab=98.78  E-value=3.9e-09  Score=84.99  Aligned_cols=48  Identities=23%  Similarity=0.360  Sum_probs=45.2

Q ss_pred             cccchhhcccchhhHhhhhhhhcccCCCChHHHHHHHHHhCcchhhhc
Q psy17504        148 QRTKRMRTSFKHHQLRTMKSYFNINQNPDAKDLKQLAQKTGLSKRVLQ  195 (196)
Q Consensus       148 ~k~rR~RT~ft~~Ql~~L~~~F~~~~~p~~~~r~~La~~lgL~~~~Vq  195 (196)
                      .++||.||+|+..|+..||..|+..+|++..+|..||++|.|+|.|||
T Consensus       102 ~RKKktRTvFSraQV~qLEs~Fe~krYLSsaeRa~LA~sLqLTETQVK  149 (268)
T KOG0485|consen  102 DRKKKTRTVFSRAQVFQLESTFELKRYLSSAERAGLAASLQLTETQVK  149 (268)
T ss_pred             cccccchhhhhHHHHHHHHHHHHHHhhhhHHHHhHHHHhhhhhhhhhh
Confidence            355679999999999999999999999999999999999999999997

>KOG0494|consensus

Probab=98.75  E-value=4.9e-09  Score=86.46  Aligned_cols=47  Identities=30%  Similarity=0.427  Sum_probs=43.4

Q ss_pred             ccchhhcccchhhHhhhhhhhcccCCCChHHHHHHHHHhCcchhhhc
Q psy17504        149 RTKRMRTSFKHHQLRTMKSYFNINQNPDAKDLKQLAQKTGLSKRVLQ  195 (196)
Q Consensus       149 k~rR~RT~ft~~Ql~~L~~~F~~~~~p~~~~r~~La~~lgL~~~~Vq  195 (196)
                      |+|+-||+||..||.+||..|...+|||...|+-||.+|.|++.+||
T Consensus       140 kRRh~RTiFT~~Qle~LEkaFkeaHYPDv~Are~la~ktelpEDRIq  186 (332)
T KOG0494|consen  140 KRRHFRTIFTSYQLEELEKAFKEAHYPDVYAREMLADKTELPEDRIQ  186 (332)
T ss_pred             ccccccchhhHHHHHHHHHHHhhccCccHHHHHHHhhhccCchhhhh
Confidence            34444999999999999999999999999999999999999999986

>KOG0842|consensus

Probab=98.74  E-value=5.1e-09  Score=89.11  Aligned_cols=49  Identities=16%  Similarity=0.296  Sum_probs=46.2

Q ss_pred             ccccchhhcccchhhHhhhhhhhcccCCCChHHHHHHHHHhCcchhhhc
Q psy17504        147 HQRTKRMRTSFKHHQLRTMKSYFNINQNPDAKDLKQLAQKTGLSKRVLQ  195 (196)
Q Consensus       147 ~~k~rR~RT~ft~~Ql~~L~~~F~~~~~p~~~~r~~La~~lgL~~~~Vq  195 (196)
                      .+++||.|..|+..|..+||+.|..++|+++.+||+||..|.||++|||
T Consensus       150 ~~~kRKrRVLFSqAQV~ELERRFrqQRYLSAPERE~LA~~LrLT~TQVK  198 (307)
T KOG0842|consen  150 KRKKRKRRVLFSQAQVYELERRFRQQRYLSAPEREHLASSLRLTPTQVK  198 (307)
T ss_pred             cccccccccccchhHHHHHHHHHHhhhccccHhHHHHHHhcCCCchhee
Confidence            4566778999999999999999999999999999999999999999997

>KOG1701|consensus

Probab=98.73  E-value=3e-09  Score=93.02  Aligned_cols=51  Identities=35%  Similarity=0.653  Sum_probs=46.9

Q ss_pred             CCChHHHHHHHHhHHHhhhhhhhhhhcceeccCCccccccceeeeccchhhh
Q psy17504          2 GISSSELVMRARDLVFHLHCFTCISCGILLTKGDLFGMRDEMIYCRPHYEIL   53 (196)
Q Consensus         2 ~i~~~~~v~~a~~~~~H~~CF~C~~C~~~L~~G~~f~~~~~~~~C~~~y~~~   53 (196)
                      +|...+...+|++.+||+.||+|.+|+++| .|..|+..++++||+.+|+..
T Consensus       283 ~V~g~~~ac~Am~~~fHv~CFtC~~C~r~L-~Gq~FY~v~~k~~CE~cyq~t  333 (468)
T KOG1701|consen  283 TVSGQGLAVEAMDQLFHVQCFTCRTCRRQL-AGQSFYQVDGKPYCEGCYQDT  333 (468)
T ss_pred             cccCcchHHHHhhhhhcccceehHhhhhhh-ccccccccCCcccchHHHHHH
Confidence            567778889999999999999999999999 799999999999999999754

>KOG0486|consensus

Probab=98.73  E-value=7.6e-09  Score=87.38  Aligned_cols=50  Identities=26%  Similarity=0.439  Sum_probs=47.0

Q ss_pred             cccccchhhcccchhhHhhhhhhhcccCCCChHHHHHHHHHhCcchhhhc
Q psy17504        146 SHQRTKRMRTSFKHHQLRTMKSYFNINQNPDAKDLKQLAQKTGLSKRVLQ  195 (196)
Q Consensus       146 ~~~k~rR~RT~ft~~Ql~~L~~~F~~~~~p~~~~r~~La~~lgL~~~~Vq  195 (196)
                      +.+|+||.||.||.+||++||..|++|.||+...||+||..++|++..|+
T Consensus       108 ki~KqrrQrthFtSqqlqele~tF~rNrypdMstrEEIavwtNlTE~rvr  157 (351)
T KOG0486|consen  108 KISKQRRQRTHFTSQQLQELEATFQRNRYPDMSTREEIAVWTNLTEARVR  157 (351)
T ss_pred             hhhhhhhhhhhhHHHHHHHHHHHHhhccCCccchhhHHHhhccccchhhh
Confidence            34588999999999999999999999999999999999999999999886

>PF00046 Homeobox: Homeobox domain not present here

Probab=98.72  E-value=5.8e-09  Score=67.42  Aligned_cols=46  Identities=37%  Similarity=0.681  Sum_probs=43.6

Q ss_pred             chhhcccchhhHhhhhhhhcccCCCChHHHHHHHHHhCcchhhhcC
Q psy17504        151 KRMRTSFKHHQLRTMKSYFNINQNPDAKDLKQLAQKTGLSKRVLQN  196 (196)
Q Consensus       151 rR~RT~ft~~Ql~~L~~~F~~~~~p~~~~r~~La~~lgL~~~~Vq~  196 (196)
                      ||.|+.||.+|+..|+..|..++||+...++.||..+||+..+|++
T Consensus         1 kr~r~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~   46 (57)
T PF00046_consen    1 KRKRTRFTKEQLKVLEEYFQENPYPSKEEREELAKELGLTERQVKN   46 (57)
T ss_dssp             SSSSSSSSHHHHHHHHHHHHHSSSCHHHHHHHHHHHHTSSHHHHHH
T ss_pred             CcCCCCCCHHHHHHHHHHHHHhcccccccccccccccccccccccc
Confidence            5689999999999999999999999999999999999999999973

; InterPro: IPR001356 The homeobox domain was first identified in a number of drosophila homeotic and segmentation proteins, but is now known to be well-conserved in many other animals, including vertebrates [, , ]. Hox genes encode homeodomain-containing transcriptional regulators that operate differential genetic programs along the anterior-posterior axis of animal bodies []. The domain binds DNA through a helix-turn-helix (HTH) structure. The HTH motif is characterised by two alpha-helices, which make intimate contacts with the DNA and are joined by a short turn. The second helix binds to DNA via a number of hydrogen bonds and hydrophobic interactions, which occur between specific side chains and the exposed bases and thymine methyl groups within the major groove of the DNA []. The first helix helps to stabilise the structure. The motif is very similar in sequence and structure in a wide range of DNA-binding proteins (e.g., cro and repressor proteins, homeotic proteins, etc.). One of the principal differences between HTH motifs in these different proteins arises from the stereo-chemical requirement for glycine in the turn which is needed to avoid steric interference of the beta-carbon with the main chain: for cro and repressor proteins the glycine appears to be mandatory, while for many of the homeotic and other DNA-binding proteins the requirement is relaxed.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2DA3_A 1LFB_A 2LFB_A 2ECB_A 2DA5_A 3D1N_O 3A03_A 2XSD_C 3CMY_A 1AHD_P ....

>KOG1701|consensus

Probab=98.59  E-value=1.2e-08  Score=89.42  Aligned_cols=50  Identities=28%  Similarity=0.632  Sum_probs=46.0

Q ss_pred             HHHHHHHHhHHHhhhhhhhhhhcceeccCCccccc-cceeeeccchhhhhhc
Q psy17504          6 SELVMRARDLVFHLHCFTCISCGILLTKGDLFGMR-DEMIYCRPHYEILRHR   56 (196)
Q Consensus         6 ~~~v~~a~~~~~H~~CF~C~~C~~~L~~G~~f~~~-~~~~~C~~~y~~~~~~   56 (196)
                      .|+++||.++.||..||+|++|++-| .|..|.+. ++++||-.||+..|+.
T Consensus       345 ~d~iLrA~GkayHp~CF~Cv~C~r~l-dgipFtvd~~n~v~Cv~dfh~kfAP  395 (468)
T KOG1701|consen  345 MDRILRALGKAYHPGCFTCVVCARCL-DGIPFTVDSQNNVYCVPDFHKKFAP  395 (468)
T ss_pred             HHHHHHhcccccCCCceEEEEecccc-CCccccccCCCceeeehhhhhhcCc
Confidence            58999999999999999999999999 78999886 6799999999999864

>smart00389 HOX Homeodomain

Probab=98.57  E-value=5e-08  Score=62.52  Aligned_cols=45  Identities=38%  Similarity=0.547  Sum_probs=42.5

Q ss_pred             hhhcccchhhHhhhhhhhcccCCCChHHHHHHHHHhCcchhhhcC
Q psy17504        152 RMRTSFKHHQLRTMKSYFNINQNPDAKDLKQLAQKTGLSKRVLQN  196 (196)
Q Consensus       152 R~RT~ft~~Ql~~L~~~F~~~~~p~~~~r~~La~~lgL~~~~Vq~  196 (196)
                      +.|+.|+..|+..|+..|..++||+...+..||..+||+..+|++
T Consensus         2 k~r~~~~~~~~~~L~~~f~~~~~P~~~~~~~la~~~~l~~~qV~~   46 (56)
T smart00389        2 RKRTSFTPEQLEELEKEFQKNPYPSREEREELAAKLGLSERQVKV   46 (56)
T ss_pred             CCCCcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHCcCHHHHHH
Confidence            567889999999999999999999999999999999999999974

DNA-binding factors that are involved in the transcriptional regulation of key developmental processes

>KOG0493|consensus

Probab=98.51  E-value=7.2e-08  Score=79.71  Aligned_cols=45  Identities=33%  Similarity=0.490  Sum_probs=43.6

Q ss_pred             chhhcccchhhHhhhhhhhcccCCCChHHHHHHHHHhCcchhhhc
Q psy17504        151 KRMRTSFKHHQLRTMKSYFNINQNPDAKDLKQLAQKTGLSKRVLQ  195 (196)
Q Consensus       151 rR~RT~ft~~Ql~~L~~~F~~~~~p~~~~r~~La~~lgL~~~~Vq  195 (196)
                      ||+||.||.+||..|++.|+.|+|+....|.+||+.|+|.+.|||
T Consensus       247 KRPRTAFtaeQL~RLK~EF~enRYlTEqRRQ~La~ELgLNEsQIK  291 (342)
T KOG0493|consen  247 KRPRTAFTAEQLQRLKAEFQENRYLTEQRRQELAQELGLNESQIK  291 (342)
T ss_pred             cCccccccHHHHHHHHHHHhhhhhHHHHHHHHHHHHhCcCHHHhh
Confidence            588999999999999999999999999999999999999999986

>cd00086 homeodomain Homeodomain; DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner

Probab=98.42  E-value=1.9e-07  Score=60.19  Aligned_cols=45  Identities=31%  Similarity=0.519  Sum_probs=42.4

Q ss_pred             hhhcccchhhHhhhhhhhcccCCCChHHHHHHHHHhCcchhhhcC
Q psy17504        152 RMRTSFKHHQLRTMKSYFNINQNPDAKDLKQLAQKTGLSKRVLQN  196 (196)
Q Consensus       152 R~RT~ft~~Ql~~L~~~F~~~~~p~~~~r~~La~~lgL~~~~Vq~  196 (196)
                      +.|+.|+..|+..|+..|..++||+..+++.||..+||++.+|++
T Consensus         2 ~~r~~~~~~~~~~Le~~f~~~~~P~~~~~~~la~~~~l~~~qV~~   46 (59)
T cd00086           2 RKRTRFTPEQLEELEKEFEKNPYPSREEREELAKELGLTERQVKI   46 (59)
T ss_pred             CCCCcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHCcCHHHHHH
Confidence            467899999999999999999999999999999999999999974

>KOG0492|consensus

Probab=98.35  E-value=2.1e-07  Score=74.66  Aligned_cols=49  Identities=18%  Similarity=0.325  Sum_probs=45.8

Q ss_pred             ccccchhhcccchhhHhhhhhhhcccCCCChHHHHHHHHHhCcchhhhc
Q psy17504        147 HQRTKRMRTSFKHHQLRTMKSYFNINQNPDAKDLKQLAQKTGLSKRVLQ  195 (196)
Q Consensus       147 ~~k~rR~RT~ft~~Ql~~L~~~F~~~~~p~~~~r~~La~~lgL~~~~Vq  195 (196)
                      .+..|++||.||..||..||+.|...+|+++.+|.+++..|.|++.|||
T Consensus       141 hk~nRkPRtPFTtqQLlaLErkfrekqYLSiaEraefSsSL~LTeTqVK  189 (246)
T KOG0492|consen  141 HKPNRKPRTPFTTQQLLALERKFREKQYLSIAERAEFSSSLELTETQVK  189 (246)
T ss_pred             cCCCCCCCCCCCHHHHHHHHHHHhHhhhhhHHHHHhhhhhhhhhhhhee
Confidence            3455778999999999999999999999999999999999999999997

>KOG0490|consensus

Probab=98.32  E-value=1e-06  Score=72.01  Aligned_cols=130  Identities=34%  Similarity=0.440  Sum_probs=92.3

Q ss_pred             CCChHHHHHHHHhHHHhhhhhhhhhhcceeccCCccccccc-eeeeccchhhhhhccccCcccccCCCCCCCCCCCCccc
Q psy17504          2 GISSSELVMRARDLVFHLHCFTCISCGILLTKGDLFGMRDE-MIYCRPHYEILRHRDYCGSAEIEQPMSPRPAPWQPTTV   80 (196)
Q Consensus         2 ~i~~~~~v~~a~~~~~H~~CF~C~~C~~~L~~G~~f~~~~~-~~~C~~~y~~~~~~~~~~~~~~~~~~~p~~~~~~~~~~   80 (196)
                      .|...|+|+++...+ |.-||.|..|...+..++++.+... +.+|..++......  ...     .+.+  ..      
T Consensus        68 ~~~ql~~ler~f~~~-h~Pd~~~r~~la~~~~~~e~rVqvwFqnrrak~r~~~~~~--~~~-----~~~~--~~------  131 (235)
T KOG0490|consen   68 TISQLDELERAFEKV-HLPCFACRECLALLLTGDEFRVQVWFQNRRAKDRKEERPL--PEG-----ENLP--DL------  131 (235)
T ss_pred             CcCHHHHHHHhhcCC-CcCccchHHHHhhcCCCCeeeeehhhhhhcHhhhhhhccc--ccc-----ccCC--CC------
Confidence            467889999999999 9999999999999989999988765 88888887654200  000     0000  00      


Q ss_pred             ccCCcccccccccCCCCCccccccceeeccccchhhhccCCccccccccccccCCCCCCCCCccccccccchhhcccchh
Q psy17504         81 QKGRPRKRKLSVDSPTPPSEDINANVMRIPSTTLEMLHSGDLSSSMESLSYESGAGNSSPGSGVHSHQRTKRMRTSFKHH  160 (196)
Q Consensus        81 ~~g~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~gs~~~~~~k~rR~RT~ft~~  160 (196)
                                   ..+..     . .  .                    ..+.    ...   .....+.++.||.++..
T Consensus       132 -------------~~~~~-----~-~--~--------------------~~~~----~~~---~~~~~~~~~~~~~~~~~  163 (235)
T KOG0490|consen  132 -------------SGTAP-----P-S--A--------------------SRDK----LDK---GPSNKKPRRPRTTFTEN  163 (235)
T ss_pred             -------------CCCCC-----c-c--c--------------------cccc----ccc---CCCccccCCCccccccc
Confidence                         00000     0 0  0                    0000    000   01234678899999999


Q ss_pred             hHhhhhhhhcccCCCChHHHHHHHHHhCcchhhhc
Q psy17504        161 QLRTMKSYFNINQNPDAKDLKQLAQKTGLSKRVLQ  195 (196)
Q Consensus       161 Ql~~L~~~F~~~~~p~~~~r~~La~~lgL~~~~Vq  195 (196)
                      |+..+...|...++|+...+++|+..+++++.+||
T Consensus       164 ~~~~~~~~~~~~~~P~~~~~~~l~~~~~~~~~~~q  198 (235)
T KOG0490|consen  164 QLEVLETVFRATPKPDADDREQLAEETGLSERVIQ  198 (235)
T ss_pred             hhHhhhhcccCCCCCchhhHHHHHHhcCCChhhhh
Confidence            99999999999999999999999999999999886

>KOG0487|consensus

Probab=98.27  E-value=3e-07  Score=78.42  Aligned_cols=50  Identities=20%  Similarity=0.327  Sum_probs=46.7

Q ss_pred             cccccchhhcccchhhHhhhhhhhcccCCCChHHHHHHHHHhCcchhhhc
Q psy17504        146 SHQRTKRMRTSFKHHQLRTMKSYFNINQNPDAKDLKQLAQKTGLSKRVLQ  195 (196)
Q Consensus       146 ~~~k~rR~RT~ft~~Ql~~L~~~F~~~~~p~~~~r~~La~~lgL~~~~Vq  195 (196)
                      ..++.|++|-.||..|+.+||+.|..|.|+....|.+|++.|+|+++|||
T Consensus       231 ~~~~~RKKRcPYTK~QtlELEkEFlfN~YitkeKR~ElSr~lNLTeRQVK  280 (308)
T KOG0487|consen  231 SARRGRKKRCPYTKHQTLELEKEFLFNMYITKEKRLELSRTLNLTERQVK  280 (308)
T ss_pred             cccccccccCCchHHHHHHHHHHHHHHHHHhHHHHHHHHHhcccchhhee
Confidence            34677788999999999999999999999999999999999999999997

>KOG2272|consensus

Probab=98.22  E-value=4.9e-07  Score=74.58  Aligned_cols=54  Identities=20%  Similarity=0.509  Sum_probs=48.6

Q ss_pred             CCChHHHHHHHHhHHHhhhhhhhhhhcceeccCCccccccceeeeccchhhhhhc
Q psy17504          2 GISSSELVMRARDLVFHLHCFTCISCGILLTKGDLFGMRDEMIYCRPHYEILRHR   56 (196)
Q Consensus         2 ~i~~~~~v~~a~~~~~H~~CF~C~~C~~~L~~G~~f~~~~~~~~C~~~y~~~~~~   56 (196)
                      |+.++|.++...+.+||..||.|+.|-.++ ++..|+--+|+.||+.||+.|+++
T Consensus        21 gF~~~e~~vns~ge~wH~~CFvCAQCf~pf-~~g~~~efEgRkYCEhDF~~LfaP   74 (332)
T KOG2272|consen   21 GFEPAEKIVNSNGELWHEQCFVCAQCFRPF-PDGIFYEFEGRKYCEHDFHVLFAP   74 (332)
T ss_pred             cCCchhhhhccCchhhHHHHHHHHHhcCcC-CCceeEEecCcccccccchhhhch
Confidence            678999999999999999999999999999 566666679999999999999874

>KOG0848|consensus

Probab=98.13  E-value=1.1e-06  Score=73.11  Aligned_cols=48  Identities=21%  Similarity=0.363  Sum_probs=44.1

Q ss_pred             cccchhhcccchhhHhhhhhhhcccCCCChHHHHHHHHHhCcchhhhc
Q psy17504        148 QRTKRMRTSFKHHQLRTMKSYFNINQNPDAKDLKQLAQKTGLSKRVLQ  195 (196)
Q Consensus       148 ~k~rR~RT~ft~~Ql~~L~~~F~~~~~p~~~~r~~La~~lgL~~~~Vq  195 (196)
                      +.+-+.|.+||..|+.+||..|..++|+.+..+.+||..|+|+|||||
T Consensus       197 RTkDKYRvVYTDhQRLELEKEfh~SryITirRKSELA~~LgLsERQVK  244 (317)
T KOG0848|consen  197 RTKDKYRVVYTDHQRLELEKEFHTSRYITIRRKSELAATLGLSERQVK  244 (317)
T ss_pred             ecccceeEEecchhhhhhhhhhccccceeeehhHHHHHhhCccHhhhh
Confidence            333457999999999999999999999999999999999999999997

>KOG0491|consensus

Probab=98.10  E-value=1.1e-06  Score=68.12  Aligned_cols=47  Identities=23%  Similarity=0.374  Sum_probs=44.5

Q ss_pred             ccchhhcccchhhHhhhhhhhcccCCCChHHHHHHHHHhCcchhhhc
Q psy17504        149 RTKRMRTSFKHHQLRTMKSYFNINQNPDAKDLKQLAQKTGLSKRVLQ  195 (196)
Q Consensus       149 k~rR~RT~ft~~Ql~~L~~~F~~~~~p~~~~r~~La~~lgL~~~~Vq  195 (196)
                      ++++.||+|+..||..|+..|+.+.|++..+|.+||..|+|++.|||
T Consensus        99 ~r~K~Rtvfs~~ql~~l~~rFe~QrYLS~~e~~ELan~L~LS~~QVK  145 (194)
T KOG0491|consen   99 RRRKARTVFSDPQLSGLEKRFERQRYLSTPERQELANALSLSETQVK  145 (194)
T ss_pred             HhhhhcccccCccccccHHHHhhhhhcccHHHHHHHHHhhhhHHHHH
Confidence            45668999999999999999999999999999999999999999997

>KOG4577|consensus

Probab=98.07  E-value=1.4e-06  Score=73.04  Aligned_cols=50  Identities=20%  Similarity=0.455  Sum_probs=45.9

Q ss_pred             HHHHHHHHhHHHhhhhhhhhhhcceeccCCccccccceeeeccchhhhhhcc
Q psy17504          6 SELVMRARDLVFHLHCFTCISCGILLTKGDLFGMRDEMIYCRPHYEILRHRD   57 (196)
Q Consensus         6 ~~~v~~a~~~~~H~~CF~C~~C~~~L~~G~~f~~~~~~~~C~~~y~~~~~~~   57 (196)
                      ..+|+++.++.||-.|..|..|..+|  ++.+..+++.+||++||-+.|++.
T Consensus        45 DrFilKvl~R~wHs~CLkCs~C~~qL--~drCFsR~~s~yCkedFfKrfGTK   94 (383)
T KOG4577|consen   45 DRFILKVLDRHWHSSCLKCSDCHDQL--ADRCFSREGSVYCKEDFFKRFGTK   94 (383)
T ss_pred             HHHHHHHHhhhhhhhhcchhhhhhHH--HHHHhhcCCceeehHHHHHHhCCc
Confidence            45899999999999999999999999  788888999999999999998754

>KOG0849|consensus

Probab=97.97  E-value=4.7e-06  Score=73.06  Aligned_cols=50  Identities=32%  Similarity=0.460  Sum_probs=46.6

Q ss_pred             cccccchhhcccchhhHhhhhhhhcccCCCChHHHHHHHHHhCcchhhhc
Q psy17504        146 SHQRTKRMRTSFKHHQLRTMKSYFNINQNPDAKDLKQLAQKTGLSKRVLQ  195 (196)
Q Consensus       146 ~~~k~rR~RT~ft~~Ql~~L~~~F~~~~~p~~~~r~~La~~lgL~~~~Vq  195 (196)
                      ..++.+|.||+|+..|+..|+..|++++||+...|++||.+++|++..|+
T Consensus       172 ~~~~~rr~rtsft~~Q~~~le~~f~rt~yP~i~~Re~La~~i~l~e~riq  221 (354)
T KOG0849|consen  172 LQRGGRRNRTSFSPSQLEALEECFQRTPYPDIVGRETLAKETGLPEPRVQ  221 (354)
T ss_pred             ccccccccccccccchHHHHHHHhcCCCCCchhhHHHHhhhccCCchHHH
Confidence            45677888999999999999999999999999999999999999998876

>KOG0844|consensus

Probab=97.92  E-value=8.2e-06  Score=69.05  Aligned_cols=49  Identities=18%  Similarity=0.299  Sum_probs=46.2

Q ss_pred             ccccchhhcccchhhHhhhhhhhcccCCCChHHHHHHHHHhCcchhhhc
Q psy17504        147 HQRTKRMRTSFKHHQLRTMKSYFNINQNPDAKDLKQLAQKTGLSKRVLQ  195 (196)
Q Consensus       147 ~~k~rR~RT~ft~~Ql~~L~~~F~~~~~p~~~~r~~La~~lgL~~~~Vq  195 (196)
                      .-+-||.||.||.+|+-.||+.|-+..|.++..|-+||..|+|+|..||
T Consensus       178 ~dqmRRYRTAFTReQIaRLEKEFyrENYVSRprRcELAAaLNLPEtTIK  226 (408)
T KOG0844|consen  178 DDQMRRYRTAFTREQIARLEKEFYRENYVSRPRRCELAAALNLPETTIK  226 (408)
T ss_pred             cHHHHHHHhhhhHHHHHHHHHHHHHhccccCchhhhHHHhhCCCcceee
Confidence            3567899999999999999999999999999999999999999999886

>KOG2272|consensus

Probab=97.87  E-value=3.3e-06  Score=69.74  Aligned_cols=49  Identities=27%  Similarity=0.478  Sum_probs=45.8

Q ss_pred             HHHHHHHHhHHHhhhhhhhhhhcceeccCCccccccceeeeccchhhhhh
Q psy17504          6 SELVMRARDLVFHLHCFTCISCGILLTKGDLFGMRDEMIYCRPHYEILRH   55 (196)
Q Consensus         6 ~~~v~~a~~~~~H~~CF~C~~C~~~L~~G~~f~~~~~~~~C~~~y~~~~~   55 (196)
                      .+.|+.|+++.||+.-|.|++|.+++ -|...+.+.|..||+.||.+|++
T Consensus       206 eervi~amgKhWHveHFvCa~CekPF-lGHrHYEkkGlaYCe~h~~qLfG  254 (332)
T KOG2272|consen  206 EERVIFAMGKHWHVEHFVCAKCEKPF-LGHRHYEKKGLAYCETHYHQLFG  254 (332)
T ss_pred             HHHHHHHhccccchhheeehhcCCcc-cchhhhhhcCchhHHHHHHHHhh
Confidence            57899999999999999999999998 68888889999999999999985

>COG5576 Homeodomain-containing transcription factor [Transcription]

Probab=97.64  E-value=5.1e-05  Score=59.16  Aligned_cols=46  Identities=22%  Similarity=0.281  Sum_probs=41.7

Q ss_pred             cchhhcccchhhHhhhhhhhcccCCCChHHHHHHHHHhCcchhhhc
Q psy17504        150 TKRMRTSFKHHQLRTMKSYFNINQNPDAKDLKQLAQKTGLSKRVLQ  195 (196)
Q Consensus       150 ~rR~RT~ft~~Ql~~L~~~F~~~~~p~~~~r~~La~~lgL~~~~Vq  195 (196)
                      .++.|+..|..|+..|++.|++++||+...|..|+..++|+++-||
T Consensus        51 ~~~~r~R~t~~Q~~vL~~~F~i~p~Ps~~~r~~L~~~lnm~~ksVq   96 (156)
T COG5576          51 PKSKRRRTTDEQLMVLEREFEINPYPSSITRIKLSLLLNMPPKSVQ   96 (156)
T ss_pred             CcccceechHHHHHHHHHHhccCCCCCHHHHHHHHHhcCCChhhhh
Confidence            4455666689999999999999999999999999999999999887

>KOG1703|consensus

Probab=97.63  E-value=1.3e-05  Score=73.05  Aligned_cols=49  Identities=35%  Similarity=0.566  Sum_probs=43.0

Q ss_pred             HHHHHHHHhHHHhhhhhhhhhhcceeccCCccccccceeeeccchhhhhh
Q psy17504          6 SELVMRARDLVFHLHCFTCISCGILLTKGDLFGMRDEMIYCRPHYEILRH   55 (196)
Q Consensus         6 ~~~v~~a~~~~~H~~CF~C~~C~~~L~~G~~f~~~~~~~~C~~~y~~~~~   55 (196)
                      .+-+|.|.+..||..||.|..|.+.| .+..|++.++.+||..||..++.
T Consensus       374 ~~~~v~a~~~~wH~~cf~C~~C~~~~-~~~~~~~~~~~pyce~~~~~~~~  422 (479)
T KOG1703|consen  374 LEEGVCALGRLWHPECFVCADCGKPL-KNSSFFESDGEPYCEDHYKKLFT  422 (479)
T ss_pred             HHhHhhhccCeechhceeeecccCCC-CCCcccccCCccchhhhHhhhcc
Confidence            35577888999999999999998888 67788889999999999999885

>KOG3802|consensus

Probab=97.62  E-value=3.8e-05  Score=67.28  Aligned_cols=47  Identities=23%  Similarity=0.426  Sum_probs=44.9

Q ss_pred             ccchhhcccchhhHhhhhhhhcccCCCChHHHHHHHHHhCcchhhhc
Q psy17504        149 RTKRMRTSFKHHQLRTMKSYFNINQNPDAKDLKQLAQKTGLSKRVLQ  195 (196)
Q Consensus       149 k~rR~RT~ft~~Ql~~L~~~F~~~~~p~~~~r~~La~~lgL~~~~Vq  195 (196)
                      |+||+||.|....+..||..|.+|+.|+..+...||.+|+|.+.||+
T Consensus       293 RkRKKRTSie~~vr~aLE~~F~~npKPt~qEIt~iA~~L~leKEVVR  339 (398)
T KOG3802|consen  293 RKRKKRTSIEVNVRGALEKHFLKNPKPTSQEITHIAESLQLEKEVVR  339 (398)
T ss_pred             cccccccceeHHHHHHHHHHHHhCCCCCHHHHHHHHHHhccccceEE
Confidence            66779999999999999999999999999999999999999999986

>KOG1044|consensus

Probab=97.45  E-value=2e-05  Score=71.71  Aligned_cols=45  Identities=29%  Similarity=0.635  Sum_probs=38.7

Q ss_pred             HHHHHhHHHhhhhhhhhhhcceeccCCccccccceeeeccchhhhhh
Q psy17504          9 VMRARDLVFHLHCFTCISCGILLTKGDLFGMRDEMIYCRPHYEILRH   55 (196)
Q Consensus         9 v~~a~~~~~H~~CF~C~~C~~~L~~G~~f~~~~~~~~C~~~y~~~~~   55 (196)
                      ++-|.++.||+.||.|..|...| . .+|...++.+||..||+..|.
T Consensus       148 ~llald~qwhv~cfkc~~c~~vL-~-gey~skdg~pyce~dy~~~fg  192 (670)
T KOG1044|consen  148 ALLALDKQWHVSCFKCKSCSAVL-N-GEYMSKDGVPYCEKDYQAKFG  192 (670)
T ss_pred             eeeeeccceeeeeeehhhhcccc-c-ceeeccCCCcchhhhhhhhcC
Confidence            44578999999999999999999 3 467778999999999988764

>KOG2252|consensus

Probab=97.32  E-value=0.00015  Score=65.82  Aligned_cols=49  Identities=27%  Similarity=0.375  Sum_probs=45.7

Q ss_pred             cccchhhcccchhhHhhhhhhhcccCCCChHHHHHHHHHhCcchhhhcC
Q psy17504        148 QRTKRMRTSFKHHQLRTMKSYFNINQNPDAKDLKQLAQKTGLSKRVLQN  196 (196)
Q Consensus       148 ~k~rR~RT~ft~~Ql~~L~~~F~~~~~p~~~~r~~La~~lgL~~~~Vq~  196 (196)
                      -+.||+|.+||..|...|...|..+++|+..+.+.|+++|+|....|.|
T Consensus       418 ~~~KKPRlVfTd~QkrTL~aiFke~~RPS~Emq~tIS~qL~L~~sTV~N  466 (558)
T KOG2252|consen  418 LQTKKPRLVFTDIQKRTLQAIFKENKRPSREMQETISQQLNLELSTVIN  466 (558)
T ss_pred             ccCCCceeeecHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCcHHHHHH
Confidence            4567789999999999999999999999999999999999999998875

>smart00132 LIM Zinc-binding domain present in Lin-11, Isl-1, Mec-3

Probab=97.29  E-value=1.1e-05  Score=47.26  Aligned_cols=29  Identities=48%  Similarity=0.902  Sum_probs=23.6

Q ss_pred             CChHHHHHHHHhHHHhhhhhhhhhhccee
Q psy17504          3 ISSSELVMRARDLVFHLHCFTCISCGILL   31 (196)
Q Consensus         3 i~~~~~v~~a~~~~~H~~CF~C~~C~~~L   31 (196)
                      |...+.++.+.+..||..||.|..|++.|
T Consensus         9 i~~~~~~~~~~~~~~H~~Cf~C~~C~~~L   37 (39)
T smart00132        9 IRGGELVLRALGKVWHPECFKCSKCGKPL   37 (39)
T ss_pred             ccCCcEEEEeCCccccccCCCCcccCCcC
Confidence            33334566778899999999999999988

Zinc-binding domain family. Some LIM domains bind protein partners via tyrosine-containing motifs. LIM domains are found in many key regulators of developmental pathways.

>KOG1044|consensus

Probab=96.89  E-value=0.00016  Score=66.01  Aligned_cols=46  Identities=30%  Similarity=0.689  Sum_probs=39.2

Q ss_pred             HHHHHHhHHHhhhhhhhhhhcceeccCCccccccceeeeccchhhh
Q psy17504          8 LVMRARDLVFHLHCFTCISCGILLTKGDLFGMRDEMIYCRPHYEIL   53 (196)
Q Consensus         8 ~v~~a~~~~~H~~CF~C~~C~~~L~~G~~f~~~~~~~~C~~~y~~~   53 (196)
                      -|+|+.++.||+.||.|..|++.|..|..|.-.+..+||-.++...
T Consensus        29 evlrv~d~~fhi~cf~c~~cg~~la~~gff~k~~~~~ygt~~c~~~   74 (670)
T KOG1044|consen   29 EVLRVNDNHFHINCFQCKKCGRNLAEGGFFTKPENRLYGTDDCRAF   74 (670)
T ss_pred             ceeEeeccccceeeeeccccCCCcccccceecccceeecccchhhh
Confidence            3788999999999999999999998888888767799998666543

>KOG1702|consensus

Probab=96.81  E-value=0.00046  Score=55.69  Aligned_cols=49  Identities=35%  Similarity=0.663  Sum_probs=36.3

Q ss_pred             ChHHHHHHHHhHHHhhhhhhhhhhcceeccCCccccccceeeeccchhhhh
Q psy17504          4 SSSELVMRARDLVFHLHCFTCISCGILLTKGDLFGMRDEMIYCRPHYEILR   54 (196)
Q Consensus         4 ~~~~~v~~a~~~~~H~~CF~C~~C~~~L~~G~~f~~~~~~~~C~~~y~~~~   54 (196)
                      .|.|.| +..+++||..||.|.+|+..|.-- .|--.+.++||..||....
T Consensus        15 YPvE~v-~cldk~whk~cfkce~c~mtlnmK-nyKgy~kkpycn~hYpkq~   63 (264)
T KOG1702|consen   15 YPVEEV-KCLDKVWHKQCFKCEVCGMTLNMK-NYKGYDKKPYCNPHYPKQV   63 (264)
T ss_pred             ccHHHH-hhHHHHHHHHhheeeeccCChhhh-hccccccCCCcCcccccce
Confidence            345544 568899999999999999988432 2222477999999997543

>KOG1168|consensus

Probab=96.32  E-value=0.0022  Score=54.28  Aligned_cols=47  Identities=30%  Similarity=0.569  Sum_probs=43.3

Q ss_pred             ccchhhcccchhhHhhhhhhhcccCCCChHHHHHHHHHhCcchhhhc
Q psy17504        149 RTKRMRTSFKHHQLRTMKSYFNINQNPDAKDLKQLAQKTGLSKRVLQ  195 (196)
Q Consensus       149 k~rR~RT~ft~~Ql~~L~~~F~~~~~p~~~~r~~La~~lgL~~~~Vq  195 (196)
                      -+||+||.+-.-..+.||.+|..++.|+......||++|+|.+.+|+
T Consensus       308 ekKRKRTSIAAPEKRsLEayFavQPRPS~EkIAaIAekLDLKKNVVR  354 (385)
T KOG1168|consen  308 EKKRKRTSIAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVR  354 (385)
T ss_pred             ccccccccccCcccccHHHHhccCCCCchhHHHHHHHhhhhhhceEE
Confidence            35678999999999999999999999999999999999999998875

>KOG1700|consensus

Probab=96.32  E-value=0.0015  Score=52.93  Aligned_cols=45  Identities=29%  Similarity=0.721  Sum_probs=37.4

Q ss_pred             HHhHHHhhhhhhhhhhcceeccCCccccccceeeeccchhhhhhcc
Q psy17504         12 ARDLVFHLHCFTCISCGILLTKGDLFGMRDEMIYCRPHYEILRHRD   57 (196)
Q Consensus        12 a~~~~~H~~CF~C~~C~~~L~~G~~f~~~~~~~~C~~~y~~~~~~~   57 (196)
                      +.+..||+.||.|..|+..|..+ .|....+.+||..++..++.+.
T Consensus       126 ~~~~~~hk~cfrc~~~~~~ls~~-~~~~~~g~l~~~~~~~~~~~~~  170 (200)
T KOG1700|consen  126 GNGLEFHKSCFRCTHCGKKLSPK-NYAALEGVLYCKHHFAQLFKGK  170 (200)
T ss_pred             hhhhhhhhhheeecccccccCCc-chhhcCCccccchhhheeecCC
Confidence            57889999999999999999654 5666789999999998876543

>KOG0483|consensus

Probab=96.29  E-value=0.0036  Score=50.62  Aligned_cols=40  Identities=20%  Similarity=0.381  Sum_probs=38.0

Q ss_pred             ccchhhHhhhhhhhcccCCCChHHHHHHHHHhCcchhhhc
Q psy17504        156 SFKHHQLRTMKSYFNINQNPDAKDLKQLAQKTGLSKRVLQ  195 (196)
Q Consensus       156 ~ft~~Ql~~L~~~F~~~~~p~~~~r~~La~~lgL~~~~Vq  195 (196)
                      .|+.+|+..||..|+.+.++....+..||..|||.++||.
T Consensus        56 Rlt~eQ~~~LE~~F~~~~~L~p~~K~~LAk~LgL~pRQVa   95 (198)
T KOG0483|consen   56 RLTSEQVKFLEKSFESEKKLEPERKKKLAKELGLQPRQVA   95 (198)
T ss_pred             cccHHHHHHhHHhhccccccChHHHHHHHHhhCCChhHHH
Confidence            4799999999999999999999999999999999999984

>KOG0847|consensus

Probab=96.07  E-value=0.003  Score=51.46  Aligned_cols=48  Identities=23%  Similarity=0.365  Sum_probs=44.2

Q ss_pred             cccchhhcccchhhHhhhhhhhcccCCCChHHHHHHHHHhCcchhhhc
Q psy17504        148 QRTKRMRTSFKHHQLRTMKSYFNINQNPDAKDLKQLAQKTGLSKRVLQ  195 (196)
Q Consensus       148 ~k~rR~RT~ft~~Ql~~L~~~F~~~~~p~~~~r~~La~~lgL~~~~Vq  195 (196)
                      .+++-.|.+|+-.|+..|+..|+..+|+-...|.+||..+|+++.+|+
T Consensus       165 G~rk~srPTf~g~qi~~le~~feqtkylaG~~ra~lA~~lgmteSqvk  212 (288)
T KOG0847|consen  165 GQRKQSRPTFTGHQIYQLERKFEQTKYLAGADRAQLAQELNMTESQVK  212 (288)
T ss_pred             ccccccCCCccchhhhhhhhhhhhhhcccchhHHHhhccccccHHHHH
Confidence            455667889999999999999999999999999999999999999985

>PF05920 Homeobox_KN: Homeobox KN domain; InterPro: IPR008422 This entry represents a homeobox transcription factor KN domain conserved from fungi to human and plants []

Probab=95.66  E-value=0.0058  Score=36.69  Aligned_cols=26  Identities=35%  Similarity=0.613  Sum_probs=20.7

Q ss_pred             ccCCCChHHHHHHHHHhCcchhhhcC
Q psy17504        171 INQNPDAKDLKQLAQKTGLSKRVLQN  196 (196)
Q Consensus       171 ~~~~p~~~~r~~La~~lgL~~~~Vq~  196 (196)
                      .++||+..+++.||..+||+..||.+
T Consensus         7 ~nPYPs~~ek~~L~~~tgls~~Qi~~   32 (40)
T PF05920_consen    7 HNPYPSKEEKEELAKQTGLSRKQISN   32 (40)
T ss_dssp             TSGS--HHHHHHHHHHHTS-HHHHHH
T ss_pred             CCCCCCHHHHHHHHHHcCCCHHHHHH
Confidence            37999999999999999999999863

; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus; PDB: 3K2A_B 2LK2_A 1X2N_A 2DMN_A.

>KOG1700|consensus

Probab=95.27  E-value=0.0098  Score=48.22  Aligned_cols=48  Identities=25%  Similarity=0.416  Sum_probs=36.6

Q ss_pred             hHHHHHHHHhHHHhhhhhhhhhhcceeccCCccccccceeeeccchhhhh
Q psy17504          5 SSELVMRARDLVFHLHCFTCISCGILLTKGDLFGMRDEMIYCRPHYEILR   54 (196)
Q Consensus         5 ~~~~v~~a~~~~~H~~CF~C~~C~~~L~~G~~f~~~~~~~~C~~~y~~~~   54 (196)
                      ..+++. ..+..||..||.|..|.+.|..+ .+...++.+||+.+|-.++
T Consensus        19 ~~e~~~-~~g~~~hk~c~~c~~~~k~l~~~-~~~~~e~~~yc~~~~~~~~   66 (200)
T KOG1700|consen   19 FVEKVQ-KDGVDFHKECFKCEKCKKTLTLS-GYSEHEGVPYCKNCHVAQF   66 (200)
T ss_pred             HHHHHh-ccCcchhhhHHhccccccccccc-cccccccccccccchHhhh
Confidence            444554 66889999999999999999554 4555899999999544444

>KOG0775|consensus

Probab=93.68  E-value=0.062  Score=45.30  Aligned_cols=38  Identities=21%  Similarity=0.441  Sum_probs=32.8

Q ss_pred             hhhHhhhhhhhcccCCCChHHHHHHHHHhCcchhhhcC
Q psy17504        159 HHQLRTMKSYFNINQNPDAKDLKQLAQKTGLSKRVLQN  196 (196)
Q Consensus       159 ~~Ql~~L~~~F~~~~~p~~~~r~~La~~lgL~~~~Vq~  196 (196)
                      +.-...|+..|..++||....+.+||+.|||+..||-|
T Consensus       185 ekSR~~LrewY~~~~YPsp~eKReLA~aTgLt~tQVsN  222 (304)
T KOG0775|consen  185 EKSRSLLREWYLQNPYPSPREKRELAEATGLTITQVSN  222 (304)
T ss_pred             HhhHHHHHHHHhcCCCCChHHHHHHHHHhCCchhhhhh
Confidence            33446788899999999999999999999999999854

>KOG0774|consensus

Probab=91.84  E-value=0.18  Score=42.39  Aligned_cols=47  Identities=21%  Similarity=0.445  Sum_probs=41.3

Q ss_pred             cchhhcccchhhHhhhhhhhc---ccCCCChHHHHHHHHHhCcchhhhcC
Q psy17504        150 TKRMRTSFKHHQLRTMKSYFN---INQNPDAKDLKQLAQKTGLSKRVLQN  196 (196)
Q Consensus       150 ~rR~RT~ft~~Ql~~L~~~F~---~~~~p~~~~r~~La~~lgL~~~~Vq~  196 (196)
                      .||+|-.|+..--+.|..+|.   .|+||+-..+++||.+-+++..||-|
T Consensus       188 arRKRRNFsK~aTeiLneyF~~h~~nPYPSee~K~eLAkqCnItvsQvsn  237 (334)
T KOG0774|consen  188 ARRKRRNFSKQATEILNEYFYSHLSNPYPSEEAKEELAKQCNITVSQVSN  237 (334)
T ss_pred             HHHhhcccchhHHHHHHHHHHHhcCCCCCcHHHHHHHHHHcCceehhhcc
Confidence            367788899999999999985   58999999999999999999988753

>KOG1146|consensus

Probab=89.32  E-value=0.36  Score=48.65  Aligned_cols=49  Identities=27%  Similarity=0.443  Sum_probs=44.8

Q ss_pred             ccccchhhcccchhhHhhhhhhhcccCCCChHHHHHHHHHhCcchhhhc
Q psy17504        147 HQRTKRMRTSFKHHQLRTMKSYFNINQNPDAKDLKQLAQKTGLSKRVLQ  195 (196)
Q Consensus       147 ~~k~rR~RT~ft~~Ql~~L~~~F~~~~~p~~~~r~~La~~lgL~~~~Vq  195 (196)
                      .-.+|+.||.++..||..|...|....||...+.|.|...++++.++|+
T Consensus       900 ~~~r~a~~~~~~d~qlk~i~~~~~~q~~~~~~~~E~l~~~~~~~~~~i~  948 (1406)
T KOG1146|consen  900 GMGRRAYRTQESDLQLKIIKACYEAQRTPTMQECEVLEEPIGLPKRVIQ  948 (1406)
T ss_pred             hhhhhhhccchhHHHHHHHHHHHhhccCChHHHHHhhcccccCCcchhH
Confidence            3455778999999999999999999999999999999999999999985

>KOG1703|consensus

Probab=87.75  E-value=0.085  Score=48.21  Aligned_cols=48  Identities=23%  Similarity=0.376  Sum_probs=39.1

Q ss_pred             HHHHHHhHHHhhhhhhhhhhcceeccCCccccccceeeeccchhhhhhc
Q psy17504          8 LVMRARDLVFHLHCFTCISCGILLTKGDLFGMRDEMIYCRPHYEILRHR   56 (196)
Q Consensus         8 ~v~~a~~~~~H~~CF~C~~C~~~L~~G~~f~~~~~~~~C~~~y~~~~~~   56 (196)
                      .++.+.+..||..+|.|.+|...+..+. |...+|.+||..+|...+..
T Consensus       317 ~~i~~~~~~~h~~~~~c~~~~~~~~~~~-~~~~~g~~~c~~~~~~~~~p  364 (479)
T KOG1703|consen  317 KVIVALGKEWHPEHFSCEVCAIVILDGG-PRELDGKILCHECFHAPFRP  364 (479)
T ss_pred             eeEeeccccccccceeeccccccccCCC-ccccCCCccHHHHHHHhhCc
Confidence            3455788999999999999999995554 46678999999999887654

>PF04967 HTH_10: HTH DNA binding domain; InterPro: IPR007050 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif

Probab=84.38  E-value=1.2  Score=28.27  Aligned_cols=38  Identities=24%  Similarity=0.427  Sum_probs=31.3

Q ss_pred             cchhhHhhhhhhhcccCC--CChHHHHHHHHHhCcchhhh
Q psy17504        157 FKHHQLRTMKSYFNINQN--PDAKDLKQLAQKTGLSKRVL  194 (196)
Q Consensus       157 ft~~Ql~~L~~~F~~~~~--p~~~~r~~La~~lgL~~~~V  194 (196)
                      +|..|++.|..+++.-.|  |-...-.+||..+|+++..|
T Consensus         1 LT~~Q~e~L~~A~~~GYfd~PR~~tl~elA~~lgis~st~   40 (53)
T PF04967_consen    1 LTDRQREILKAAYELGYFDVPRRITLEELAEELGISKSTV   40 (53)
T ss_pred             CCHHHHHHHHHHHHcCCCCCCCcCCHHHHHHHhCCCHHHH
Confidence            478899999999987776  66667789999999998654

This entry represents the HTH DNA binding domain found in Halobacterium salinarium (Halobacterium halobium) and described as a putative bacterio-opsin activator.

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	196
2dmq_A	80	Solution Structure Of The Homeobox Domain Of LimHOM		1e-18
2rgt_A	169	Crystal Structure Of Lhx3 Lim Domains 1 And 2 With		2e-07
2jtn_A	182	Nmr Solution Structure Of A Ldb1-Lid:lhx3-Lim Compl		4e-07
3mmk_A	169	The Structural Basis For Partial Redundancy In A Cl		1e-06
2da1_A	70	Solution Structure Of The First Homeobox Domain Of		6e-05
2dfy_X	195	Crystal Structure Of A Cyclized Protein Fusion Of L		2e-04
1rut_X	188	Complex Of Lmo4 Lim Domains 1 And 2 With The Ldb1 L		2e-04

>pdb|2DMQ|A Chain A, Solution Structure Of The Homeobox Domain Of LimHOMEOBOX Protein Lhx9 Length = 80

Iteration: 1
 Score = 89.4 bits (220), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 42/45 (93%), Positives = 43/45 (95%)
Query: 151 KRMRTSFKHHQLRTMKSYFNINQNPDAKDLKQLAQKTGLSKRVLQ 195
           KRMRTSFKHHQLRTMKSYF IN NPDAKDLKQLAQKTGL+KRVLQ
Sbjct: 8   KRMRTSFKHHQLRTMKSYFAINHNPDAKDLKQLAQKTGLTKRVLQ 52

>pdb|2RGT|A Chain A, Crystal Structure Of Lhx3 Lim Domains 1 And 2 With The Binding Domain Of Isl1 Length = 169

Iteration: 1
 Score = 52.0 bits (123), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 23/55 (41%), Positives = 33/55 (60%), Gaps = 1/55 (1%)
Query: 1   MGISSSELVMRARDLVFHLHCFTCISCGILLTKGDLFG-MRDEMIYCRPHYEILR 54
           +GI  +++V RA+D V+HLHCF C+ C   L  GD F  M D  + C+  YE  +
Sbjct: 73  LGIPPTQVVRRAQDFVYHLHCFACVVCKRQLATGDEFYLMEDSRLVCKADYETAK 127

>pdb|2JTN|A Chain A, Nmr Solution Structure Of A Ldb1-Lid:lhx3-Lim Complex Length = 182

Iteration: 1
 Score = 51.2 bits (121), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 23/56 (41%), Positives = 33/56 (58%), Gaps = 1/56 (1%)
Query: 1   MGISSSELVMRARDLVFHLHCFTCISCGILLTKGDLFG-MRDEMIYCRPHYEILRH 55
           +GI  +++V RA+D V+HLHCF C+ C   L  GD F  M D  + C+  YE  + 
Sbjct: 127 LGIPPTQVVRRAQDFVYHLHCFACVVCKRQLATGDEFYLMEDSRLVCKADYETAKQ 182

>pdb|3MMK|A Chain A, The Structural Basis For Partial Redundancy In A Class Of Transcription Factors, The Lim-Homeodomain Proteins, In Neural Cell Type Specification Length = 169

Iteration: 1
 Score = 49.7 bits (117), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 23/55 (41%), Positives = 32/55 (58%), Gaps = 1/55 (1%)
Query: 2   GISSSELVMRARDLVFHLHCFTCISCGILLTKGDLFG-MRDEMIYCRPHYEILRH 55
           GI  +++V +A+D V+HLHCF CI C   L  GD F  M D  + C+  YE  + 
Sbjct: 74  GIPPTQVVRKAQDFVYHLHCFACIICNRQLATGDEFYLMEDGRLVCKEDYETAKQ 128

>pdb|2DA1|A Chain A, Solution Structure Of The First Homeobox Domain Of At- Binding Transcription Factor 1 (Atbf1) Length = 70

Iteration: 1
 Score = 43.9 bits (102), Expect = 6e-05,   Method: Compositional matrix adjust.
 Identities = 18/45 (40%), Positives = 31/45 (68%)
Query: 151 KRMRTSFKHHQLRTMKSYFNINQNPDAKDLKQLAQKTGLSKRVLQ 195
           KR RT     QLR ++ YF+IN +P  + +K++A K+GL ++V++
Sbjct: 8   KRPRTRITDDQLRVLRQYFDINNSPSEEQIKEMADKSGLPQKVIK 52

>pdb|2DFY|X Chain X, Crystal Structure Of A Cyclized Protein Fusion Of Lmo4 Lim Domains 1 And 2 With The Lim Interacting Domain Of Ldb1 Length = 195

Iteration: 1
 Score = 42.0 bits (97), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 21/44 (47%), Positives = 28/44 (63%)
Query: 3   ISSSELVMRARDLVFHLHCFTCISCGILLTKGDLFGMRDEMIYC 46
           I +SELVMRA+  V+HL CFTC +C   L  GD F   +  ++C
Sbjct: 77  IPASELVMRAQGNVYHLKCFTCSTCRNRLVPGDRFHYINGSLFC 120

>pdb|1RUT|X Chain X, Complex Of Lmo4 Lim Domains 1 And 2 With The Ldb1 Lid Domain Length = 188

Iteration: 1
 Score = 42.0 bits (97), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 21/44 (47%), Positives = 28/44 (63%)
Query: 3   ISSSELVMRARDLVFHLHCFTCISCGILLTKGDLFGMRDEMIYC 46
           I +SELVMRA+  V+HL CFTC +C   L  GD F   +  ++C
Sbjct: 79  IPASELVMRAQGNVYHLKCFTCSTCRNRLVPGDRFHYINGSLFC 122

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	196
2l3k_A	123	Rhombotin-2, linker, LIM domain-binding protein 1;	2e-21
2da3_A	80	Alpha-fetoprotein enhancer binding protein; homeob	5e-21
2da1_A	70	Alpha-fetoprotein enhancer binding protein; homeob	1e-19
2xjy_A	131	Rhombotin-2; oncoprotein, T-cell leukemia, proto-o	3e-19
2xjy_A	131	Rhombotin-2; oncoprotein, T-cell leukemia, proto-o	6e-09
1rut_X	188	Flinc4, fusion protein of LMO4 protein and LIM dom	4e-19
1rut_X	188	Flinc4, fusion protein of LMO4 protein and LIM dom	6e-07
2rgt_A	169	Fusion of LIM/homeobox protein LHX3, linker, INSU	5e-19
2rgt_A	169	Fusion of LIM/homeobox protein LHX3, linker, INSU	1e-06
2dmq_A	80	LIM/homeobox protein LHX9; homeobox domain, three	9e-19
1bw5_A	66	ISL-1HD, insulin gene enhancer protein ISL-1; DNA-	3e-17
2da2_A	70	Alpha-fetoprotein enhancer binding protein; homeob	3e-17
2jtn_A	182	LIM domain-binding protein 1, LIM/homeobox protein	2e-16
2jtn_A	182	LIM domain-binding protein 1, LIM/homeobox protein	5e-07
1au7_A	146	Protein PIT-1, GHF-1; complex (DNA-binding protein	2e-16
1wi3_A	71	DNA-binding protein SATB2; homeodomain, helix-turn	2e-15
1e3o_C	160	Octamer-binding transcription factor 1; transcript	1e-14
2dms_A	80	Homeobox protein OTX2; homeobox domain, three heli	3e-12
2xqn_T	126	Testin, TESS; metal-binding protein, cytoskeleton,	4e-12
2xqn_T	126	Testin, TESS; metal-binding protein, cytoskeleton,	3e-08
1x61_A	72	Thyroid receptor interacting protein 6; LIM domain	4e-12
1x6a_A	81	LIMK-2, LIM domain kinase 2; LIM-kinase 2, zinc fi	6e-12
3l1p_A	155	POU domain, class 5, transcription factor 1; POU,	1e-11
2xsd_C	164	POU domain, class 3, transcription factor 1; trans	1e-11
3nau_A	66	Zinc fingers and homeoboxes protein 2; ZHX2, corep	2e-11
2dn0_A	76	Zinc fingers and homeoboxes protein 3; triple home	2e-11
3f6q_B	72	LIM and senescent cell antigen-like-containing dom	4e-11
1g47_A	77	Pinch protein; LIM domain, Zn finger, cell adhesio	9e-11
1v6g_A	81	Actin binding LIM protein 2; LIM domain, zinc bind	2e-10
2ehe_A	82	Four and A half LIM domains 3; FHL-3, skeletal mus	7e-10
2egq_A	77	FHL1 protein; LIM domain, four and A half LIM doma	1e-09
2cup_A	101	Skeletal muscle LIM-protein 1; four and half LIM d	1e-09
2cup_A	101	Skeletal muscle LIM-protein 1; four and half LIM d	5e-08
3nar_A	96	ZHX1, zinc fingers and homeoboxes protein 1; corep	2e-09
1x63_A	82	Skeletal muscle LIM-protein 1; LIM domain, four an	3e-09
3d1n_I	151	POU domain, class 6, transcription factor 1; prote	3e-09
2ecb_A	89	Zinc fingers and homeoboxes protein 1; homeobox do	5e-09
1x4k_A	72	Skeletal muscle LIM-protein 3; LIM domain, structu	8e-09
1wyh_A	72	SLIM 2, skeletal muscle LIM-protein 2; structural	9e-09
2cuq_A	80	Four and A half LIM domains 3; structural genomics	1e-08
2da5_A	75	Zinc fingers and homeoboxes protein 3; homeobox do	1e-08
2e19_A	64	Transcription factor 8; homeobox domain, structura	1e-08
2dmp_A	89	Zinc fingers and homeoboxes protein 2; homeobox do	1e-08
2cur_A	69	Skeletal muscle LIM-protein 1; four and A half LIM	3e-08
2d8y_A	91	Eplin protein; LIM domain, epithelial protein LOST	3e-08
2d8z_A	70	Four and A half LIM domains 2; skeletal muscle LIM	4e-08
2da7_A	71	Zinc finger homeobox protein 1B; homeobox domain,	5e-08
1a7i_A	81	QCRP2 (LIM1); LIM domain containing proteins, meta	5e-08
1m3v_A	122	FLIN4, fusion of the LIM interacting domain of LDB	8e-08
1m3v_A	122	FLIN4, fusion of the LIM interacting domain of LDB	8e-05
2dj7_A	80	Actin-binding LIM protein 3; LIM domain, Zn bindin	1e-07
1nyp_A	66	Pinch protein; LIM domain, protein recognition, ce	1e-07
2dar_A	90	PDZ and LIM domain protein 5; enigma homolog prote	2e-07
1x64_A	89	Alpha-actinin-2 associated LIM protein; LIM domain	3e-07
2dlo_A	81	Thyroid receptor-interacting protein 6; LIM domain	3e-07
2hi3_A	73	Homeodomain-only protein; transcription; NMR {Mus	3e-07
2d8x_A	70	Protein pinch; LIM domain, pinch protein, structur	4e-07
1x62_A	79	C-terminal LIM domain protein 1; PDZ and LIM domai	5e-07
1j2o_A	114	FLIN2, fusion of rhombotin-2 and LIM domain-bindin	5e-07
1x3h_A	80	Leupaxin; paxillin family, protein-protein interac	5e-07
2l4z_A	123	DNA endonuclease RBBP8, LIM domain transcription L	5e-07
1x4l_A	72	Skeletal muscle LIM-protein 3; LIM domain, structu	6e-07
2co8_A	82	NEDD9 interacting protein with calponin homology a	7e-07
1iml_A	76	CRIP, cysteine rich intestinal protein; metal-bind	2e-06
1b8t_A	192	Protein (CRP1); LIM domain, muscle differentiation	2e-06
1b8t_A	192	Protein (CRP1); LIM domain, muscle differentiation	3e-05
1x68_A	76	FHL5 protein; four-and-A-half LIM protein 5, zinc	2e-06
2cu8_A	76	Cysteine-rich protein 2; CRP2, CRIP2, ESP1 protein	3e-06
2d5v_A	164	Hepatocyte nuclear factor 6; transcription factor,	1e-05
1wig_A	73	KIAA1808 protein; LIM domain, zinc finger, metal-b	7e-05
2ecc_A	76	Homeobox and leucine zipper protein homez; homeobo	1e-04
1mnm_C	87	Protein (MAT alpha-2 transcriptional repressor); t	1e-04
2k40_A	67	Homeobox expressed in ES cells 1; thermostable hom	2e-04
1fjl_A	81	Paired protein; DNA-binding protein, paired BOX, t	2e-04
1akh_A	61	Protein (mating-type protein A-1); complex (TWO DN	3e-04
1wh5_A	80	ZF-HD homeobox family protein; structural genomics	3e-04
1uhs_A	72	HOP, homeodomain only protein; structural genomics	3e-04
2h8r_A	221	Hepatocyte nuclear factor 1-beta; trasncription fa	4e-04
2da4_A	80	Hypothetical protein DKFZP686K21156; homeobox doma	5e-04
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	6e-04
2dmt_A	80	Homeobox protein BARH-like 1; homeobox domain, thr	6e-04
2cor_A	79	Pinch protein; LIM domain, particularly interestin	7e-04

>2da3_A Alpha-fetoprotein enhancer binding protein; homeobox domain, three helices with the DNA binding helix- turn-helix motif, structural genomics; NMR {Homo sapiens} Length = 80

 Score = 81.8 bits (202), Expect = 5e-21
 Identities = 24/62 (38%), Positives = 35/62 (56%)

Query: 134 GAGNSSPGSGVHSHQRTKRMRTSFKHHQLRTMKSYFNINQNPDAKDLKQLAQKTGLSKRV 193
           G+  SS G+G    QR KR+RT+    QL  +   + ++ NP  K L  +A + GL KRV
Sbjct: 1   GSSGSSGGTGGEEPQRDKRLRTTITPEQLEILYQKYLLDSNPTRKMLDHIAHEVGLKKRV 60

Query: 194 LQ 195
           +Q
Sbjct: 61  VQ 62

>2da1_A Alpha-fetoprotein enhancer binding protein; homeobox domain, three helices with the DNA binding helix- turn-helix motif, structural genomics; NMR {Homo sapiens} Length = 70

 Score = 77.8 bits (192), Expect = 1e-19
 Identities = 19/50 (38%), Positives = 32/50 (64%)

Query: 146 SHQRTKRMRTSFKHHQLRTMKSYFNINQNPDAKDLKQLAQKTGLSKRVLQ 195
           S    KR RT     QLR ++ YF+IN +P  + +K++A K+GL ++V++
Sbjct: 3   SGSSGKRPRTRITDDQLRVLRQYFDINNSPSEEQIKEMADKSGLPQKVIK 52

>2xjy_A Rhombotin-2; oncoprotein, T-cell leukemia, proto-oncogene, transcription, developmental protein; 2.40A {Homo sapiens} PDB: 2xjz_A Length = 131

 Score = 78.6 bits (194), Expect = 3e-19
 Identities = 16/50 (32%), Positives = 24/50 (48%)

Query: 2   GISSSELVMRARDLVFHLHCFTCISCGILLTKGDLFGMRDEMIYCRPHYE 51
            I + E+ MR +D V+HL CF C +C      GD + + +  I C     
Sbjct: 75  RIRAYEMTMRVKDKVYHLECFKCAACQKHFCVGDRYLLINSDIVCEQDIY 124

>2xjy_A Rhombotin-2; oncoprotein, T-cell leukemia, proto-oncogene, transcription, developmental protein; 2.40A {Homo sapiens} PDB: 2xjz_A Length = 131

 Score = 51.3 bits (123), Expect = 6e-09
 Identities = 15/55 (27%), Positives = 20/55 (36%), Gaps = 2/55 (3%)

Query: 9  VMRARDLVFHLHCFTCISCGILLT-KGDLFGMRDEMIYCRPHYEILR-HRDYCGS 61
           ++A D  +H  C +C  CG  L   G     +     CR  Y  L      C S
Sbjct: 17 FLKAIDQYWHEDCLSCDLCGCRLGEVGRRLYYKLGRKLCRRDYLRLFGQDGLCAS 71

>1rut_X Flinc4, fusion protein of LMO4 protein and LIM domain- binding protein 1; B-tandem zipper, protein binding; 1.30A {Mus musculus} SCOP: g.39.1.3 g.39.1.3 g.39.1.3 g.39.1.3 PDB: 2dfy_X 2xjz_I 2xjy_B Length = 188

 Score = 80.1 bits (197), Expect = 4e-19
 Identities = 26/91 (28%), Positives = 38/91 (41%), Gaps = 3/91 (3%)

Query: 2   GISSSELVMRARDLVFHLHCFTCISCGILLTKGDLFGMRDEMIYCRPHYEIL---RHRDY 58
            I +SELVMRA+  V+HL CFTC +C   L  GD F   +  ++C           H + 
Sbjct: 78  SIPASELVMRAQGNVYHLKCFTCSTCRNRLVPGDRFHYINGSLFCEHDRPTALINGHLNS 137

Query: 59  CGSAEIEQPMSPRPAPWQPTTVQKGRPRKRK 89
            GS              +PT +      + +
Sbjct: 138 GGSGGSGGSGGDVMVVGEPTLMGGEFGDEDE 168

>1rut_X Flinc4, fusion protein of LMO4 protein and LIM domain- binding protein 1; B-tandem zipper, protein binding; 1.30A {Mus musculus} SCOP: g.39.1.3 g.39.1.3 g.39.1.3 g.39.1.3 PDB: 2dfy_X 2xjz_I 2xjy_B Length = 188

 Score = 46.9 bits (111), Expect = 6e-07
 Identities = 15/49 (30%), Positives = 19/49 (38%), Gaps = 1/49 (2%)

Query: 7  ELVMRARDLVFHLHCFTCISCGILLT-KGDLFGMRDEMIYCRPHYEILR 54
            ++ A D  +H  C  C SC   L   G     +  MI CR  Y  L 
Sbjct: 18 RFLLYAMDSYWHSRCLKCSSCQAQLGDIGTSSYTKSGMILCRNDYIRLF 66

>2rgt_A Fusion of LIM/homeobox protein LHX3, linker, INSU enhancer protein ISL-1; protein-protein complex, LIM domain, Zn finger, activator, D binding; 2.05A {Mus musculus} PDB: 3mmk_A Length = 169

 Score = 79.1 bits (195), Expect = 5e-19
 Identities = 30/95 (31%), Positives = 41/95 (43%), Gaps = 10/95 (10%)

Query: 2   GISSSELVMRARDLVFHLHCFTCISCGILLTKGDLFG-MRDEMIYCRPHYEILR--HRDY 58
           GI  +++V RA+D V+HLHCF C+ C   L  GD F  M D  + C+  YE  +      
Sbjct: 74  GIPPTQVVRRAQDFVYHLHCFACVVCKRQLATGDEFYLMEDSRLVCKADYETAKQGGSGG 133

Query: 59  CGSAEIEQPMSPRPAPWQ-------PTTVQKGRPR 86
            G +    PM               P  VQ  +P 
Sbjct: 134 SGGSGGGTPMVAASPERHDGGLQANPVEVQSYQPP 168

>2rgt_A Fusion of LIM/homeobox protein LHX3, linker, INSU enhancer protein ISL-1; protein-protein complex, LIM domain, Zn finger, activator, D binding; 2.05A {Mus musculus} PDB: 3mmk_A Length = 169

 Score = 46.0 bits (109), Expect = 1e-06
 Identities = 11/45 (24%), Positives = 20/45 (44%), Gaps = 2/45 (4%)

Query: 9  VMRARDLVFHLHCFTCISCGILLTKGDLFGMRDEMIYCRPHYEIL 53
          +++A D  +H  C  C  C + L   +    R E +YC+  +   
Sbjct: 21 ILKALDRHWHSKCLKCSDCHVPL--AERCFSRGESVYCKDDFFKR 63

>2dmq_A LIM/homeobox protein LHX9; homeobox domain, three helices with the DNA binding helix- turn-helix motif, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 80

 Score = 76.0 bits (187), Expect = 9e-19
 Identities = 43/50 (86%), Positives = 44/50 (88%)

Query: 146 SHQRTKRMRTSFKHHQLRTMKSYFNINQNPDAKDLKQLAQKTGLSKRVLQ 195
           S    KRMRTSFKHHQLRTMKSYF IN NPDAKDLKQLAQKTGL+KRVLQ
Sbjct: 3   SGSSGKRMRTSFKHHQLRTMKSYFAINHNPDAKDLKQLAQKTGLTKRVLQ 52

>1bw5_A ISL-1HD, insulin gene enhancer protein ISL-1; DNA-binding protein, homeodomain, LIM domain; NMR {Rattus norvegicus} SCOP: a.4.1.1 Length = 66

 Score = 71.6 bits (176), Expect = 3e-17
 Identities = 19/47 (40%), Positives = 29/47 (61%)

Query: 149 RTKRMRTSFKHHQLRTMKSYFNINQNPDAKDLKQLAQKTGLSKRVLQ 195
           +T R+RT     QL T+++ +  N  PDA   +QL + TGLS RV++
Sbjct: 2   KTTRVRTVLNEKQLHTLRTCYAANPRPDALMKEQLVEMTGLSPRVIR 48

>2da2_A Alpha-fetoprotein enhancer binding protein; homeobox domain, three helices with the DNA binding helix- turn-helix motif, structural genomics; NMR {Homo sapiens} Length = 70

 Score = 71.2 bits (175), Expect = 3e-17
 Identities = 15/50 (30%), Positives = 25/50 (50%)

Query: 146 SHQRTKRMRTSFKHHQLRTMKSYFNINQNPDAKDLKQLAQKTGLSKRVLQ 195
           S    +  RT F  +QLR ++ +F+ N  P   + +QL+    L  RV+ 
Sbjct: 3   SGSSGRSSRTRFTDYQLRVLQDFFDANAYPKDDEFEQLSNLLNLPTRVIV 52

>2jtn_A LIM domain-binding protein 1, LIM/homeobox protein LHX3; intramolecular (fusion) protein-protein complex, protein binding/transcription complex; NMR {Mus musculus} Length = 182

 Score = 72.3 bits (177), Expect = 2e-16
 Identities = 23/51 (45%), Positives = 31/51 (60%), Gaps = 1/51 (1%)

Query: 2   GISSSELVMRARDLVFHLHCFTCISCGILLTKGDLFG-MRDEMIYCRPHYE 51
           GI  +++V RA+D V+HLHCF C+ C   L  GD F  M D  + C+  YE
Sbjct: 128 GIPPTQVVRRAQDFVYHLHCFACVVCKRQLATGDEFYLMEDSRLVCKADYE 178

>2jtn_A LIM domain-binding protein 1, LIM/homeobox protein LHX3; intramolecular (fusion) protein-protein complex, protein binding/transcription complex; NMR {Mus musculus} Length = 182

 Score = 46.8 bits (111), Expect = 5e-07
 Identities = 11/43 (25%), Positives = 20/43 (46%), Gaps = 2/43 (4%)

Query: 9   VMRARDLVFHLHCFTCISCGILLTKGDLFGMRDEMIYCRPHYE 51
           +++A D  +H  C  C  C + L   +    R E +YC+  + 
Sbjct: 75  ILKALDRHWHSKCLKCSDCHVPL--AERCFSRGESVYCKDDFF 115

>1au7_A Protein PIT-1, GHF-1; complex (DNA-binding protein/DNA), pituitary, CPHD, POU domain, transcription factor, transcription/DNA complex; HET: DNA; 2.30A {Rattus norvegicus} SCOP: a.4.1.1 a.35.1.1 Length = 146

 Score = 71.6 bits (175), Expect = 2e-16
 Identities = 14/90 (15%), Positives = 42/90 (46%)

Query: 106 VMRIPSTTLEMLHSGDLSSSMESLSYESGAGNSSPGSGVHSHQRTKRMRTSFKHHQLRTM 165
           + R  +  L   ++  L + +     E+    +     V +++R ++ RT+        +
Sbjct: 43  ICRFENLQLSFKNACKLKAILSKWLEEAEQVGALYNEKVGANERKRKRRTTISIAAKDAL 102

Query: 166 KSYFNINQNPDAKDLKQLAQKTGLSKRVLQ 195
           + +F  +  P ++++ ++A++  L K V++
Sbjct: 103 ERHFGEHSKPSSQEIMRMAEELNLEKEVVR 132

>1wi3_A DNA-binding protein SATB2; homeodomain, helix-turn-helix, riken structural genomics/proteomics initiative, RSGI, structural genomics; NMR {Homo sapiens} SCOP: a.4.1.1 Length = 71

 Score = 67.1 bits (164), Expect = 2e-15
 Identities = 11/52 (21%), Positives = 21/52 (40%), Gaps = 1/52 (1%)

Query: 146 SHQRTKRMRTSFKHHQLRTMKSYF-NINQNPDAKDLKQLAQKTGLSKRVLQN 196
           S     R RT      L  ++S+  ++   PD + +  L+ +  L K  +  
Sbjct: 3   SGSSGPRSRTKISLEALGILQSFIHDVGLYPDQEAIHTLSAQLDLPKHTIIK 54

>1e3o_C Octamer-binding transcription factor 1; transcription factor, POU domain, dimer, DNA binding; 1.9A {Homo sapiens} SCOP: a.4.1.1 a.35.1.1 PDB: 1gt0_C 1hf0_A* 1cqt_A* 1o4x_A 1oct_C* 1pou_A 1pog_A 1hdp_A Length = 160

 Score = 67.3 bits (164), Expect = 1e-14
 Identities = 18/87 (20%), Positives = 42/87 (48%), Gaps = 2/87 (2%)

Query: 111 STTLEMLHSGDLSSSMESLS--YESGAGNSSPGSGVHSHQRTKRMRTSFKHHQLRTMKSY 168
            + L+ L    L+ +  +LS      + ++    G+    R ++ RTS + +    ++  
Sbjct: 60  MSKLKPLLEKWLNDAEANLSSDSSLSSPSALNSPGIEGLSRRRKKRTSIETNIRVALEKS 119

Query: 169 FNINQNPDAKDLKQLAQKTGLSKRVLQ 195
           F  NQ P ++D+  +A++  + K V++
Sbjct: 120 FMENQKPTSEDITLIAEQLNMEKEVIR 146

>2dms_A Homeobox protein OTX2; homeobox domain, three helices with the DNA binding helix- turn-helix motif, structural genomics, NPPSFA; NMR {Mus musculus} Length = 80

 Score = 58.6 bits (142), Expect = 3e-12
 Identities = 14/50 (28%), Positives = 25/50 (50%)

Query: 146 SHQRTKRMRTSFKHHQLRTMKSYFNINQNPDAKDLKQLAQKTGLSKRVLQ 195
           S    +R RT+F   QL  +++ F   + PD    +++A K  L +  +Q
Sbjct: 3   SGSSGRRERTTFTRAQLDVLEALFAKTRYPDIFMREEVALKINLPESRVQ 52

>2xqn_T Testin, TESS; metal-binding protein, cytoskeleton, focal adhesion, acrosom; 2.62A {Homo sapiens} Length = 126

 Score = 59.7 bits (145), Expect = 4e-12
 Identities = 11/52 (21%), Positives = 18/52 (34%), Gaps = 3/52 (5%)

Query: 2   GISSSELVMRARDLVFHLH--CFTCISCGILLTKGDLFGMRDEMIYCRPHYE 51
            I      +   +  +H    CF C  C   L  G  F   + M++C    +
Sbjct: 72  AIDPEVQRVTYNNFSWHASTECFLCSCCSKCLI-GQKFMPVEGMVFCSVECK 122

>2xqn_T Testin, TESS; metal-binding protein, cytoskeleton, focal adhesion, acrosom; 2.62A {Homo sapiens} Length = 126

 Score = 49.3 bits (118), Expect = 3e-08
 Identities = 12/45 (26%), Positives = 22/45 (48%), Gaps = 1/45 (2%)

Query: 9  VMRARDLVFHLHCFTCISCGILLTKGDLFGMRDEMIYCRPHYEIL 53
            +A +  +HL  F C  C  +L  G+++ M ++   C+P Y   
Sbjct: 18 YTQAENQNWHLKHFCCFDCDSILA-GEIYVMVNDKPVCKPCYVKN 61

>1x61_A Thyroid receptor interacting protein 6; LIM domain, OPA-interacting protein 1, zyxin related protein 1 (ZRP-1), structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: g.39.1.3 g.39.1.3 Length = 72

 Score = 58.2 bits (141), Expect = 4e-12
 Identities = 16/60 (26%), Positives = 22/60 (36%), Gaps = 2/60 (3%)

Query: 2  GISSSELVMRARDLVFHLHCFTCISCGILLTKGDLFGMRDEMIYCRPHYEILRHR-DYCG 60
           +      + A D VFH+ CF C +C   L +G  F   +   YC   Y          G
Sbjct: 14 DVVGDGAGVVALDRVFHVGCFVCSTCRAQL-RGQHFYAVERRAYCEGCYVATLESGPSSG 72

>1x6a_A LIMK-2, LIM domain kinase 2; LIM-kinase 2, zinc finger domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: g.39.1.3 g.39.1.3 Length = 81

 Score = 58.3 bits (141), Expect = 6e-12
 Identities = 12/47 (25%), Positives = 23/47 (48%), Gaps = 1/47 (2%)

Query: 6  SELVMRARDLVFHLHCFTCISCGILLTKGDLFGMRDE-MIYCRPHYE 51
          +   M A +  +H  CF C+SC +++  GD + +     +YC   + 
Sbjct: 26 TGPFMVAGEFKYHPECFACMSCKVIIEDGDAYALVQHATLYCGKCHN 72

>3l1p_A POU domain, class 5, transcription factor 1; POU, transcription factor DNA complex, pore, stem cells; HET: DNA; 2.80A {Mus musculus} PDB: 1ocp_A Length = 155

 Score = 59.4 bits (143), Expect = 1e-11
 Identities = 14/75 (18%), Positives = 31/75 (41%), Gaps = 2/75 (2%)

Query: 121 DLSSSMESLSYESGAGNSSPGSGVHSHQRTKRMRTSFKHHQLRTMKSYFNINQNPDAKDL 180
            L   +E           S    +   ++  R RTS ++    ++++ F  +  P  + +
Sbjct: 69  LLEKWVEEADNNENLQEISKSETLVQARK--RKRTSIENRVRWSLETMFLKSPKPSLQQI 126

Query: 181 KQLAQKTGLSKRVLQ 195
             +A + GL K V++
Sbjct: 127 THIANQLGLEKDVVR 141

>2xsd_C POU domain, class 3, transcription factor 1; transcription-DNA complex, SOX; 2.05A {Mus musculus} Length = 164

 Score = 59.3 bits (143), Expect = 1e-11
 Identities = 21/95 (22%), Positives = 40/95 (42%), Gaps = 10/95 (10%)

Query: 111 STTLEMLHSGDLS-SSMESLS---------YESGAGNSSPGSGVHSHQRTKRMRTSFKHH 160
            TT+    +  LS  +M  L           +S +G+ +    + +  R ++ RTS +  
Sbjct: 50  QTTICRFEALQLSFKNMCKLKPLLNKWLEETDSSSGSPTNLDKIAAQGRKRKKRTSIEVG 109

Query: 161 QLRTMKSYFNINQNPDAKDLKQLAQKTGLSKRVLQ 195
               ++S+F     P A ++  LA    L K V++
Sbjct: 110 VKGALESHFLKCPKPSAHEITGLADSLQLEKEVVR 144

>3nau_A Zinc fingers and homeoboxes protein 2; ZHX2, corepressor, homeodomain, domain swapping, structural oxford protein production facility, OPPF; 2.70A {Homo sapiens} Length = 66

 Score = 56.3 bits (136), Expect = 2e-11
 Identities = 10/49 (20%), Positives = 22/49 (44%)

Query: 148 QRTKRMRTSFKHHQLRTMKSYFNINQNPDAKDLKQLAQKTGLSKRVLQN 196
                        Q+  +K+ F  +Q PD  ++ +L + TGL++  ++ 
Sbjct: 2   AHHHHHHRKKTKEQIAHLKASFLQSQFPDDAEVYRLIEVTGLARSEIKK 50

>2dn0_A Zinc fingers and homeoboxes protein 3; triple homeobox 1 protein, KIAA0395, TIX1, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 76

 Score = 56.3 bits (136), Expect = 2e-11
 Identities = 18/56 (32%), Positives = 27/56 (48%), Gaps = 2/56 (3%)

Query: 141 GSGVHSHQRTKRMRTSFKHHQLRTMKSYFNINQNPDAKDLKQLAQKTGLSKRVLQN 196
           GS   S     + + S  H QL  +K  F  NQ P   +++ L + TGLS R ++ 
Sbjct: 1   GSSGSSGASIYKNKKS--HEQLSALKGSFCRNQFPGQSEVEHLTKVTGLSTREVRK 54

>3f6q_B LIM and senescent cell antigen-like-containing domain protein 1; ILK, integrin-linked kinase, pinch, ankyrin repeat, ANK, IPP; 1.60A {Homo sapiens} PDB: 2kbx_B 3ixe_B Length = 72

 Score = 55.5 bits (134), Expect = 4e-11
 Identities = 12/52 (23%), Positives = 24/52 (46%), Gaps = 1/52 (1%)

Query: 2  GISSSELVMRARDLVFHLHCFTCISCGILLTKGDLFGMRDEMIYCRPHYEIL 53
          G + +E ++ +   ++H  CF C  C     +G  F   +   YC   +++L
Sbjct: 20 GFAPAEKIVNSNGELYHEQCFVCAQCFQQFPEGL-FYEFEGRKYCEHDFQML 70

>1g47_A Pinch protein; LIM domain, Zn finger, cell adhesion; NMR {Homo sapiens} SCOP: g.39.1.3 g.39.1.3 Length = 77

 Score = 54.7 bits (132), Expect = 9e-11
 Identities = 11/51 (21%), Positives = 22/51 (43%), Gaps = 1/51 (1%)

Query: 3  ISSSELVMRARDLVFHLHCFTCISCGILLTKGDLFGMRDEMIYCRPHYEIL 53
           + +E ++ +   ++H  CF C  C        LF   +   YC   +++L
Sbjct: 21 FAPAEKIVNSNGELYHEQCFVCAQCFQQFP-EGLFYEFEGRKYCEHDFQML 70

>1v6g_A Actin binding LIM protein 2; LIM domain, zinc binding domain, ablim2, structural genomics, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: g.39.1.3 g.39.1.3 Length = 81

 Score = 54.0 bits (130), Expect = 2e-10
 Identities = 10/43 (23%), Positives = 15/43 (34%)

Query: 9  VMRARDLVFHLHCFTCISCGILLTKGDLFGMRDEMIYCRPHYE 51
          V+ A    +H  CF C  C +    GD      +   C+    
Sbjct: 29 VVSALGKTYHPDCFVCAVCRLPFPPGDRVTFNGKECMCQKCSL 71

>2ehe_A Four and A half LIM domains 3; FHL-3, skeletal muscle LIM- protein 2, SLIM 2, FHL3, SLIM2, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 82

 Score = 52.5 bits (126), Expect = 7e-10
 Identities = 13/49 (26%), Positives = 17/49 (34%), Gaps = 1/49 (2%)

Query: 3  ISSSELVMRARDLVFHLHCFTCISCGILLTKGDLFGMRDEMIYCRPHYE 51
          I      +   D  FH  CF C  C   L   + F  +D  + C   Y 
Sbjct: 25 IGHDSRELFYEDRHFHEGCFRCCRCQRSLA-DEPFTCQDSELLCNDCYC 72

>2egq_A FHL1 protein; LIM domain, four and A half LIM domains protein 1, skeletal muscle LIM- protein 1, SLIM 1, structural genomics NPPSFA; NMR {Homo sapiens} Length = 77

 Score = 52.1 bits (125), Expect = 1e-09
 Identities = 12/51 (23%), Positives = 18/51 (35%), Gaps = 1/51 (1%)

Query: 1  MGISSSELVMRARDLVFHLHCFTCISCGILLTKGDLFGMRDEMIYCRPHYE 51
           G      V+      +H +CF C  C + L     F    E +YC    +
Sbjct: 26 TGFGKGSSVVAYEGQSWHDYCFHCKKCSVNLA-NKRFVFHQEQVYCPDCAK 75

>2cup_A Skeletal muscle LIM-protein 1; four and half LIM domains protein 1, LIM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: g.39.1.3 g.39.1.3 g.39.1.3 Length = 101

 Score = 52.4 bits (126), Expect = 1e-09
 Identities = 11/49 (22%), Positives = 18/49 (36%), Gaps = 1/49 (2%)

Query: 3  ISSSELVMRARDLVFHLHCFTCISCGILLTKGDLFGMRDEMIYCRPHYE 51
          I +    +  ++  +H  CF C  C   L   + F  +D  I C     
Sbjct: 15 IGADSKEVHYKNRFWHDTCFRCAKCLHPLA-NETFVAKDNKILCNKCTT 62

>2cup_A Skeletal muscle LIM-protein 1; four and half LIM domains protein 1, LIM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: g.39.1.3 g.39.1.3 g.39.1.3 Length = 101

 Score = 48.2 bits (115), Expect = 5e-08
 Identities = 7/27 (25%), Positives = 13/27 (48%)

Query: 2   GISSSELVMRARDLVFHLHCFTCISCG 28
            I + +  +  +  V+H  CF+  S G
Sbjct: 75  AIVAGDQNVEYKGTVWHKDCFSGPSSG 101

>3nar_A ZHX1, zinc fingers and homeoboxes protein 1; corepressor, homeodomain, structural genomics, oxford production facility, OPPF, transcription; 2.60A {Homo sapiens} Length = 96

 Score = 51.7 bits (123), Expect = 2e-09
 Identities = 14/71 (19%), Positives = 28/71 (39%)

Query: 126 MESLSYESGAGNSSPGSGVHSHQRTKRMRTSFKHHQLRTMKSYFNINQNPDAKDLKQLAQ 185
           M    +   +G      G      +          QL  +KS F   Q P  ++  +LA+
Sbjct: 1   MAHHHHHHSSGLEVLFQGPAPKSGSTGKICKKTPEQLHMLKSAFVRTQWPSPEEYDKLAK 60

Query: 186 KTGLSKRVLQN 196
           ++GL++  + +
Sbjct: 61  ESGLARTDIVS 71

>1x63_A Skeletal muscle LIM-protein 1; LIM domain, four and A half LIM domains protein 1, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: g.39.1.3 g.39.1.3 Length = 82

 Score = 51.2 bits (123), Expect = 3e-09
 Identities = 13/49 (26%), Positives = 23/49 (46%), Gaps = 1/49 (2%)

Query: 3  ISSSELVMRARDLVFHLHCFTCISCGILLTKGDLFGMRDEMIYCRPHYE 51
          I + +  +  +  V+H  CFTC +C  ++     F  + E  YC   +E
Sbjct: 25 IVAGDQNVEYKGTVWHKDCFTCSNCKQVIG-TGSFFPKGEDFYCVTCHE 72

>3d1n_I POU domain, class 6, transcription factor 1; protein-DNA complex, helix-turn-helix (HTH), DNA-binding, homeobox, nucleus, transcription regulation; 2.51A {Homo sapiens} Length = 151

 Score = 52.7 bits (126), Expect = 3e-09
 Identities = 13/99 (13%), Positives = 35/99 (35%), Gaps = 13/99 (13%)

Query: 110 PSTTLEMLHSGDLS-SSMESL------------SYESGAGNSSPGSGVHSHQRTKRMRTS 156
             + +      D++  S + L                    +          + ++ RTS
Sbjct: 40  SQSAISRFEKLDITPKSAQKLKPVLEKWLNEAELRNQEGQQNLMEFVGGEPSKKRKRRTS 99

Query: 157 FKHHQLRTMKSYFNINQNPDAKDLKQLAQKTGLSKRVLQ 195
           F    +  + +YF  N  P  +++ ++A++    + V++
Sbjct: 100 FTPQAIEALNAYFEKNPLPTGQEITEMAKELNYDREVVR 138

>2ecb_A Zinc fingers and homeoboxes protein 1; homeobox domain, transcription factor, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: a.4.1.1 Length = 89

 Score = 50.4 bits (120), Expect = 5e-09
 Identities = 14/61 (22%), Positives = 30/61 (49%), Gaps = 4/61 (6%)

Query: 136 GNSSPGSGVHSHQRTKRMRTSFKHHQLRTMKSYFNINQNPDAKDLKQLAQKTGLSKRVLQ 195
           G+S       + Q+ K  +T+    QLR +++ F  +     ++L +L  +T L++R + 
Sbjct: 1   GSSGSSGPDFTPQKFKE-KTA---EQLRVLQASFLNSSVLTDEELNRLRAQTKLTRREID 56

Query: 196 N 196
            
Sbjct: 57  A 57

>1x4k_A Skeletal muscle LIM-protein 3; LIM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: g.39.1.3 g.39.1.3 Length = 72

 Score = 49.3 bits (118), Expect = 8e-09
 Identities = 13/49 (26%), Positives = 18/49 (36%), Gaps = 1/49 (2%)

Query: 3  ISSSELVMRARDLVFHLHCFTCISCGILLTKGDLFGMRDEMIYCRPHYE 51
          I      M  +   +H  CF C  C   +     F  +D   +C P YE
Sbjct: 15 IMPGTRKMEYKGSSWHETCFICHRCQQPIG-TKSFIPKDNQNFCVPCYE 62

>1wyh_A SLIM 2, skeletal muscle LIM-protein 2; structural genomics, riken structural genomics/proteomics initiative, RSGI, NPPSFA; NMR {Homo sapiens} SCOP: g.39.1.3 g.39.1.3 Length = 72

 Score = 49.3 bits (118), Expect = 9e-09
 Identities = 13/49 (26%), Positives = 16/49 (32%), Gaps = 1/49 (2%)

Query: 3  ISSSELVMRARDLVFHLHCFTCISCGILLTKGDLFGMRDEMIYCRPHYE 51
          +      +      +H HCF C  C   L     F       YC P YE
Sbjct: 15 VMPGSRKLEYGGQTWHEHCFLCSGCEQPLG-SRSFVPDKGAHYCVPCYE 62

>2cuq_A Four and A half LIM domains 3; structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: g.39.1.3 g.39.1.3 Length = 80

 Score = 49.3 bits (118), Expect = 1e-08
 Identities = 16/53 (30%), Positives = 19/53 (35%), Gaps = 2/53 (3%)

Query: 9  VMRARDLVFHLHCFTCISCGILLTKGDLFGMRDEMIYCRPHYEILRHRDYCGS 61
           +  RD  +H  C  C  C   L  G  F  RDE  YC   +  L       S
Sbjct: 29 GVTYRDQPWHRECLVCTGCQTPLA-GQQFTSRDEDPYCVACFGEL-FASGPSS 79

>2da5_A Zinc fingers and homeoboxes protein 3; homeobox domain, three helices with the DNA binding helix- turn-helix motif, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 75

 Score = 49.1 bits (117), Expect = 1e-08
 Identities = 14/51 (27%), Positives = 26/51 (50%), Gaps = 2/51 (3%)

Query: 146 SHQRTKRMRTSFKHHQLRTMKSYFNINQNPDAKDLKQLAQKTGLSKRVLQN 196
           S   TK    +    QLR ++S F  N  P  ++L +L  +T +++R + +
Sbjct: 5   SSGPTKYKERA--PEQLRALESSFAQNPLPLDEELDRLRSETKMTRREIDS 53

>2e19_A Transcription factor 8; homeobox domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 64

 Score = 48.9 bits (116), Expect = 1e-08
 Identities = 10/36 (27%), Positives = 21/36 (58%)

Query: 160 HQLRTMKSYFNINQNPDAKDLKQLAQKTGLSKRVLQ 195
           + L  +K+Y+ +N  P A++L ++A    L   V++
Sbjct: 13  NLLSLLKAYYALNAQPSAEELSKIADSVNLPLDVVK 48

>2dmp_A Zinc fingers and homeoboxes protein 2; homeobox domain, three helices with the DNA binding helix- turn-helix motif, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 89

 Score = 49.2 bits (117), Expect = 1e-08
 Identities = 12/61 (19%), Positives = 25/61 (40%), Gaps = 2/61 (3%)

Query: 136 GNSSPGSGVHSHQRTKRMRTSFKHHQLRTMKSYFNINQNPDAKDLKQLAQKTGLSKRVLQ 195
           G+S            K    +    Q++ ++  F  +  P   +L +L  +T LS+R + 
Sbjct: 1   GSSGSSGAYPDFAPQKFKEKT--QGQVKILEDSFLKSSFPTQAELDRLRVETKLSRREID 58

Query: 196 N 196
           +
Sbjct: 59  S 59

>2cur_A Skeletal muscle LIM-protein 1; four and A half LIM domains protein 1, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: g.39.1.3 g.39.1.3 Length = 69

 Score = 47.8 bits (114), Expect = 3e-08
 Identities = 12/43 (27%), Positives = 20/43 (46%), Gaps = 1/43 (2%)

Query: 9  VMRARDLVFHLHCFTCISCGILLTKGDLFGMRDEMIYCRPHYE 51
           +  +D  +H  CF C++C   L  G  F   ++  YC   Y+
Sbjct: 19 GITYQDQPWHADCFVCVTCSKKLA-GQRFTAVEDQYYCVDCYK 60

>2d8y_A Eplin protein; LIM domain, epithelial protein LOST in neoplasm, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: g.39.1.3 g.39.1.3 Length = 91

 Score = 48.3 bits (115), Expect = 3e-08
 Identities = 16/44 (36%), Positives = 22/44 (50%), Gaps = 1/44 (2%)

Query: 10 MRARDLVFHLHCFTCISCGILLTKGDLFGMRDEMIYCRPHYEIL 53
          + A   VFH+ CF C  C   L+ G  +      IYC+PH+  L
Sbjct: 31 LLANQQVFHISCFRCSYCNNKLSLGT-YASLHGRIYCKPHFNQL 73

>2d8z_A Four and A half LIM domains 2; skeletal muscle LIM-protein 3, LIM-domain protein DRAL, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: g.39.1.3 g.39.1.3 Length = 70

 Score = 47.3 bits (113), Expect = 4e-08
 Identities = 15/53 (28%), Positives = 23/53 (43%), Gaps = 2/53 (3%)

Query: 9  VMRARDLVFHLHCFTCISCGILLTKGDLFGMRDEMIYCRPHYEILRHRDYCGS 61
           +  R+  +H  CF C +C   L+ G  F  RD+  YC   +  L +     S
Sbjct: 19 GVTYREQPWHKECFVCTACRKQLS-GQRFTARDDFAYCLNCFCDL-YASGPSS 69

>2da7_A Zinc finger homeobox protein 1B; homeobox domain, three helices with the DNA binding helix- turn-helix motif, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 71

 Score = 47.5 bits (112), Expect = 5e-08
 Identities = 10/50 (20%), Positives = 26/50 (52%), Gaps = 1/50 (2%)

Query: 146 SHQRTKRMRTSFKHHQLRTMKSYFNINQNPDAKDLKQLAQKTGLSKRVLQ 195
           S   +      +K H +  +K+Y+ +N  P++ +L +++   GL +  ++
Sbjct: 2   SSGSSGSPINPYKDH-MSVLKAYYAMNMEPNSDELLKISIAVGLPQEFVK 50

>1a7i_A QCRP2 (LIM1); LIM domain containing proteins, metal-binding protein, zinc finger; NMR {Coturnix japonica} SCOP: g.39.1.3 g.39.1.3 PDB: 2o10_A Length = 81

 Score = 47.4 bits (113), Expect = 5e-08
 Identities = 11/41 (26%), Positives = 17/41 (41%), Gaps = 1/41 (2%)

Query: 10 MRARDLVFHLHCFTCISCGILLTKGDLFGMRDEMIYCRPHY 50
          ++     FH  CF C+ C   L       + D  +YC+  Y
Sbjct: 23 VQCDGRSFHRCCFLCMVCRKNLDSTT-VAIHDAEVYCKSCY 62

>1m3v_A FLIN4, fusion of the LIM interacting domain of LDB1 and the N-terminal LIM domain of LMO4...; fusion protein, LMO proteins, metal binding protein; NMR {Mus musculus} SCOP: g.39.1.3 g.39.1.3 Length = 122

 Score = 48.1 bits (114), Expect = 8e-08
 Identities = 16/54 (29%), Positives = 20/54 (37%), Gaps = 1/54 (1%)

Query: 9  VMRARDLVFHLHCFTCISCGILLT-KGDLFGMRDEMIYCRPHYEILRHRDYCGS 61
          ++ A D  +H  C  C SC   L   G     +  MI CR  Y  L      G 
Sbjct: 20 LLYAMDSYWHSRCLKCSSCQAQLGDIGTSSYTKSGMILCRNDYIRLFGNSGAGG 73

>1m3v_A FLIN4, fusion of the LIM interacting domain of LDB1 and the N-terminal LIM domain of LMO4...; fusion protein, LMO proteins, metal binding protein; NMR {Mus musculus} SCOP: g.39.1.3 g.39.1.3 Length = 122

 Score = 40.0 bits (93), Expect = 8e-05
 Identities = 7/37 (18%), Positives = 9/37 (24%)

Query: 17  FHLHCFTCISCGILLTKGDLFGMRDEMIYCRPHYEIL 53
                   +  G     G  FG  DE +  R      
Sbjct: 77  HMGSGGDVMVVGEPTLMGGEFGDEDERLITRLENTQF 113

>2dj7_A Actin-binding LIM protein 3; LIM domain, Zn binding protein, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: g.39.1.3 g.39.1.3 Length = 80

 Score = 46.3 bits (110), Expect = 1e-07
 Identities = 13/43 (30%), Positives = 22/43 (51%), Gaps = 2/43 (4%)

Query: 9  VMRARDLVFHLHCFTCISCGILLTKGDLFGMRDEMIYCRPHYE 51
           + A D  +H+ CF C +C ++LT    +  +D + YC   Y 
Sbjct: 30 SLLALDKQWHVSCFKCQTCSVILTGE--YISKDGVPYCESDYH 70

>1nyp_A Pinch protein; LIM domain, protein recognition, cell adhesion; NMR {Homo sapiens} SCOP: g.39.1.3 g.39.1.3 PDB: 1u5s_B Length = 66

 Score = 46.1 bits (110), Expect = 1e-07
 Identities = 13/45 (28%), Positives = 17/45 (37%), Gaps = 1/45 (2%)

Query: 9  VMRARDLVFHLHCFTCISCGILLTKGDLFGMRDEMIYCRPHYEIL 53
          V+ A    +H+  F C  C      G     R  + YC  HY  L
Sbjct: 19 VVNAMGKQWHVEHFVCAKCEKPFL-GHRHYERKGLAYCETHYNQL 62

>2dar_A PDZ and LIM domain protein 5; enigma homolog protein, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: g.39.1.3 g.39.1.3 Length = 90

 Score = 46.3 bits (110), Expect = 2e-07
 Identities = 10/43 (23%), Positives = 14/43 (32%), Gaps = 1/43 (2%)

Query: 9  VMRARDLVFHLHCFTCISCGILLTKGDLFGMRDEMIYCRPHYE 51
           + A    +H   F C  C   +     F      +YC   YE
Sbjct: 39 FLVALGKSWHPEEFNCAHCKNTMA-YIGFVEEKGALYCELCYE 80

>1x64_A Alpha-actinin-2 associated LIM protein; LIM domain, PDZ and LIM domain 3, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: g.39.1.3 g.39.1.3 Length = 89

 Score = 45.6 bits (108), Expect = 3e-07
 Identities = 14/43 (32%), Positives = 20/43 (46%), Gaps = 1/43 (2%)

Query: 9  VMRARDLVFHLHCFTCISCGILLTKGDLFGMRDEMIYCRPHYE 51
          V++ARD   H  CF C  C + L +   F   +  +YC  H  
Sbjct: 39 VVKARDKYRHPECFVCADCNLNLKQKGYF-FVEGELYCETHAR 80

>2dlo_A Thyroid receptor-interacting protein 6; LIM domain, OPA-interacting protein 1, zyxin related protein 1 (ZRP-1), structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: g.39.1.3 g.39.1.3 Length = 81

 Score = 45.4 bits (108), Expect = 3e-07
 Identities = 11/43 (25%), Positives = 17/43 (39%)

Query: 9  VMRARDLVFHLHCFTCISCGILLTKGDLFGMRDEMIYCRPHYE 51
          ++RA    +H  CFTC+ C   L            I+C   + 
Sbjct: 29 ILRAMGKAYHPGCFTCVVCHRGLDGIPFTVDATSQIHCIEDFH 71

>2hi3_A Homeodomain-only protein; transcription; NMR {Mus musculus} SCOP: a.4.1.1 Length = 73

 Score = 45.1 bits (107), Expect = 3e-07
 Identities = 11/47 (23%), Positives = 24/47 (51%), Gaps = 1/47 (2%)

Query: 150 TKRMRTSFKHHQLRTMKSYFN-INQNPDAKDLKQLAQKTGLSKRVLQ 195
           + +  +     Q+  ++  FN +N++PD   L  +A + GL++   Q
Sbjct: 2   SAQTVSGPTEDQVEILEYNFNKVNKHPDPTTLCLIAAEAGLTEEQTQ 48

>2d8x_A Protein pinch; LIM domain, pinch protein, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: g.39.1.3 g.39.1.3 Length = 70

 Score = 44.7 bits (106), Expect = 4e-07
 Identities = 12/43 (27%), Positives = 18/43 (41%), Gaps = 1/43 (2%)

Query: 9  VMRARDLVFHLHCFTCISCGILLTKGDLFGMRDEMIYCRPHYE 51
          V++A +  +H  CF C  C  +L     F        CRP + 
Sbjct: 19 VIKAMNNSWHPECFRCDLCQEVLADIG-FVKNAGRHLCRPCHN 60

>1x62_A C-terminal LIM domain protein 1; PDZ and LIM domain protein 1, LIM domain protein CLP-36, contractIle protein, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: g.39.1.3 g.39.1.3 Length = 79

 Score = 44.7 bits (106), Expect = 5e-07
 Identities = 13/43 (30%), Positives = 19/43 (44%), Gaps = 1/43 (2%)

Query: 9  VMRARDLVFHLHCFTCISCGILLTKGDLFGMRDEMIYCRPHYE 51
           ++ RD   H  C+ C  CG  L +   F   ++ IYC  H  
Sbjct: 29 FVKLRDRHRHPECYVCTDCGTNLKQKGHF-FVEDQIYCEKHAR 70

>1j2o_A FLIN2, fusion of rhombotin-2 and LIM domain-binding protein 1; LIM-interaction-domain (LID), metal binding protein; NMR {Mus musculus} SCOP: g.39.1.3 g.39.1.3 Length = 114

 Score = 45.8 bits (108), Expect = 5e-07
 Identities = 14/63 (22%), Positives = 19/63 (30%), Gaps = 2/63 (3%)

Query: 9  VMRARDLVFHLHCFTCISCGILLT-KGDLFGMRDEMIYCRPHYEILRHRDYCGSAEIEQP 67
           ++A D  +H  C +C  CG  L   G     +     CR  Y  L              
Sbjct: 18 FLKAIDQYWHEDCLSCDLCGCRLGEVGRRLYYKLGRKLCRRDYLRL-GGSGGHMGSGGDV 76

Query: 68 MSP 70
          M  
Sbjct: 77 MVV 79

>1x3h_A Leupaxin; paxillin family, protein-protein interaction, LIM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: g.39.1.3 g.39.1.3 Length = 80

 Score = 44.6 bits (106), Expect = 5e-07
 Identities = 15/46 (32%), Positives = 19/46 (41%), Gaps = 1/46 (2%)

Query: 9  VMRARDLVFHLHCFTCISCGILLTKGDLFGMRDEMIYCRPHYEILR 54
           + A D V+H  CF C  C    + G  F   D   +C  HY   R
Sbjct: 29 YLSAMDTVWHPECFVCGDCFTSFSTGS-FFELDGRPFCELHYHHRR 73

>2l4z_A DNA endonuclease RBBP8, LIM domain transcription LMO4; protein-protein interaction, LIM-interaction DOM LMO4, RBBP8/CTIP, LIM-only protein; HET: DNA; NMR {Homo sapiens} Length = 123

 Score = 45.9 bits (108), Expect = 5e-07
 Identities = 14/44 (31%), Positives = 18/44 (40%), Gaps = 1/44 (2%)

Query: 9   VMRARDLVFHLHCFTCISCGILLT-KGDLFGMRDEMIYCRPHYE 51
           ++ A D  +H  C  C SC   L   G     +  MI CR  Y 
Sbjct: 76  LLYAMDSYWHSRCLKCSSCQAQLGDIGTSSYTKSGMILCRNDYI 119

>1x4l_A Skeletal muscle LIM-protein 3; LIM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: g.39.1.3 g.39.1.3 Length = 72

 Score = 44.4 bits (105), Expect = 6e-07
 Identities = 10/47 (21%), Positives = 17/47 (36%), Gaps = 1/47 (2%)

Query: 9  VMRARDLVFHLHCFTCISCGILLTKGDLFGMRDEMIYCRPHYEILRH 55
           +   +  +H  CF C  C + L  G  F    + I C    + +  
Sbjct: 23 YISFEERQWHNDCFNCKKCSLSLV-GRGFLTERDDILCPDCGKDISG 68

>2co8_A NEDD9 interacting protein with calponin homology and LIM domains; zinc finger protein, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: g.39.1.3 g.39.1.3 Length = 82

 Score = 44.6 bits (105), Expect = 7e-07
 Identities = 12/47 (25%), Positives = 14/47 (29%), Gaps = 1/47 (2%)

Query: 10 MRARDLVFHLHCFTCISCGILLTKGDL-FGMRDEMIYCRPHYEILRH 55
          +      FH  CF C +C   L  G       D   YC  H      
Sbjct: 31 LCVNGHFFHRSCFRCHTCEATLWPGGYEQHPGDGHFYCLQHLPQTDS 77

>1iml_A CRIP, cysteine rich intestinal protein; metal-binding protein, LIM domain protein; NMR {Rattus rattus} SCOP: g.39.1.3 g.39.1.3 Length = 76

 Score = 43.5 bits (103), Expect = 2e-06
 Identities = 12/45 (26%), Positives = 17/45 (37%), Gaps = 2/45 (4%)

Query: 10 MRARDLVFHLHCFTCISCGILLTKGDLFGMRDEMIYC-RPHYEIL 53
          + +    +H  C  C  CG  LT G      +   YC  P Y  +
Sbjct: 16 VTSLGKDWHRPCLKCEKCGKTLTSGG-HAEHEGKPYCNHPCYSAM 59

>1b8t_A Protein (CRP1); LIM domain, muscle differentiation, contractIle; NMR {Gallus gallus} SCOP: g.39.1.3 g.39.1.3 g.39.1.3 g.39.1.3 PDB: 1ibi_A 1qli_A 1cxx_A 1ctl_A 2o13_A Length = 192

 Score = 45.4 bits (107), Expect = 2e-06
 Identities = 12/44 (27%), Positives = 16/44 (36%), Gaps = 1/44 (2%)

Query: 10  MRARDLVFHLHCFTCISCGILLTKGDLFGMRDEMIYCRPHYEIL 53
           +      +H  CF C  CG  L        +D  IYC+  Y   
Sbjct: 131 VIGAGKSWHKSCFRCAKCGKSLESTT-LADKDGEIYCKGCYAKN 173

>1b8t_A Protein (CRP1); LIM domain, muscle differentiation, contractIle; NMR {Gallus gallus} SCOP: g.39.1.3 g.39.1.3 g.39.1.3 g.39.1.3 PDB: 1ibi_A 1qli_A 1cxx_A 1ctl_A 2o13_A Length = 192

 Score = 41.9 bits (98), Expect = 3e-05
 Identities = 11/45 (24%), Positives = 17/45 (37%), Gaps = 1/45 (2%)

Query: 9  VMRARDLVFHLHCFTCISCGILLTKGDLFGMRDEMIYCRPHYEIL 53
           ++     FH  CF C+ C   L       +  + IYC+  Y   
Sbjct: 22 EVQCEGSSFHKSCFLCMVCKKNLD-STTVAVHGDEIYCKSCYGKK 65

>1x68_A FHL5 protein; four-and-A-half LIM protein 5, zinc finger domain, AN actin- interacting protein, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: g.39.1.3 g.39.1.3 Length = 76

 Score = 42.9 bits (101), Expect = 2e-06
 Identities = 11/46 (23%), Positives = 21/46 (45%), Gaps = 1/46 (2%)

Query: 9  VMRARDLVFHLHCFTCISCGILLTKGDLFGMRDEMIYCRPHYEILR 54
           +  +D  +H  CF C  C + L  G  F  +++ I+C+     + 
Sbjct: 23 FICFQDSQWHSECFNCGKCSVSLV-GKGFLTQNKEIFCQKCGSGMD 67

>2cu8_A Cysteine-rich protein 2; CRP2, CRIP2, ESP1 protein, zinc-binding, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: g.39.1.3 g.39.1.3 Length = 76

 Score = 42.8 bits (101), Expect = 3e-06
 Identities = 12/45 (26%), Positives = 17/45 (37%), Gaps = 2/45 (4%)

Query: 10 MRARDLVFHLHCFTCISCGILLTKGDLFGMRDEMIYC-RPHYEIL 53
          + +    +H  C  C  C   LT G      D   +C +P Y  L
Sbjct: 25 VSSLGKDWHKFCLKCERCSKTLTPGG-HAEHDGKPFCHKPCYATL 68

>2d5v_A Hepatocyte nuclear factor 6; transcription factor, transcription-DNA complex; 2.00A {Rattus norvegicus} PDB: 1s7e_A Length = 164

 Score = 42.9 bits (100), Expect = 1e-05
 Identities = 15/70 (21%), Positives = 25/70 (35%)

Query: 127 ESLSYESGAGNSSPGSGVHSHQRTKRMRTSFKHHQLRTMKSYFNINQNPDAKDLKQLAQK 186
            S    +         G       K+ R  F   Q RT+ + F  N+ P  +    ++Q+
Sbjct: 74  MSALRLAACKRKEQEHGKDRGNTPKKPRLVFTDVQRRTLHAIFKENKRPSKELQITISQQ 133

Query: 187 TGLSKRVLQN 196
            GL    + N
Sbjct: 134 LGLELSTVSN 143

>1wig_A KIAA1808 protein; LIM domain, zinc finger, metal-binding protein, structural genomics, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: g.39.1.3 g.39.1.3 Length = 73

 Score = 38.9 bits (90), Expect = 7e-05
 Identities = 9/38 (23%), Positives = 19/38 (50%)

Query: 9  VMRARDLVFHLHCFTCISCGILLTKGDLFGMRDEMIYC 46
          V+ A +  +H  C  C+ CG +  +G+   ++   I+ 
Sbjct: 19 VLEAGEKHYHPSCALCVRCGQMFAEGEEMYLQGSSIWH 56

>2ecc_A Homeobox and leucine zipper protein homez; homeobox domain, transcription factor, leucine zipper- containing factor, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: a.4.1.1 Length = 76

 Score = 38.4 bits (89), Expect = 1e-04
 Identities = 12/47 (25%), Positives = 20/47 (42%)

Query: 150 TKRMRTSFKHHQLRTMKSYFNINQNPDAKDLKQLAQKTGLSKRVLQN 196
           +          QL  +KS+F   Q    +D ++L Q TGL +  +  
Sbjct: 3   SGSSGKRKTKEQLAILKSFFLQCQWARREDYQKLEQITGLPRPEIIQ 49

>1mnm_C Protein (MAT alpha-2 transcriptional repressor); transcription regulation, transcriptional repression, DNA- binding protein; HET: DNA; 2.25A {Saccharomyces cerevisiae} SCOP: a.4.1.1 Length = 87

 Score = 38.3 bits (89), Expect = 1e-04
 Identities = 16/76 (21%), Positives = 32/76 (42%), Gaps = 4/76 (5%)

Query: 124 SSMESLSYESGAGNSSPGSGVHSHQRTKRMRTSFKHHQLRTMKSYFNINQN---PDAKDL 180
            + ++ S +    N      ++   +  R    F    +R ++S+F  N      D K L
Sbjct: 2   LTQKNKSADGLVFNVVTQDMINKSTKPYR-GHRFTKENVRILESWFAKNIENPYLDTKGL 60

Query: 181 KQLAQKTGLSKRVLQN 196
           + L + T LS+  ++N
Sbjct: 61  ENLMKNTSLSRIQIKN 76

>2k40_A Homeobox expressed in ES cells 1; thermostable homeodomain variant, DNA binding protein, developmental protein, disease mutation, DNA-binding; NMR {Homo sapiens} Length = 67

 Score = 37.7 bits (88), Expect = 2e-04
 Identities = 14/40 (35%), Positives = 23/40 (57%)

Query: 151 KRMRTSFKHHQLRTMKSYFNINQNPDAKDLKQLAQKTGLS 190
           +R RT+F  +Q+  +++ F +N  P    L+ LAQK  L 
Sbjct: 2   RRPRTAFTQNQIEVLENVFRVNCYPGIDILEDLAQKLNLE 41

>1fjl_A Paired protein; DNA-binding protein, paired BOX, transcription regulation; HET: DNA; 2.00A {Drosophila melanogaster} SCOP: a.4.1.1 PDB: 3a01_B Length = 81

 Score = 37.3 bits (87), Expect = 2e-04
 Identities = 20/59 (33%), Positives = 29/59 (49%), Gaps = 2/59 (3%)

Query: 132 ESGAGNSSPGSGVHSHQRTKRMRTSFKHHQLRTMKSYFNINQNPDAKDLKQLAQKTGLS 190
           +     S PG  +   QR  R RT+F   QL  ++  F   Q PD    ++LAQ+T L+
Sbjct: 2   DISDCESEPGIALKRKQR--RSRTTFSASQLDELERAFERTQYPDIYTREELAQRTNLT 58

>1akh_A Protein (mating-type protein A-1); complex (TWO DNA-binding proteins/DNA), complex, DNA- binding protein, DNA; HET: DNA; 2.50A {Saccharomyces cerevisiae} SCOP: a.4.1.1 PDB: 1f43_A 1yrn_A* Length = 61

 Score = 36.8 bits (86), Expect = 3e-04
 Identities = 7/45 (15%), Positives = 25/45 (55%)

Query: 148 QRTKRMRTSFKHHQLRTMKSYFNINQNPDAKDLKQLAQKTGLSKR 192
           +++ + ++S        ++  F   Q+ ++K+ +++A+K G++  
Sbjct: 3   EKSPKGKSSISPQARAFLEEVFRRKQSLNSKEKEEVAKKCGITPL 47

>1wh5_A ZF-HD homeobox family protein; structural genomics, zinc finger homeobox family protein, riken structural genomics/proteomics initiative; NMR {Arabidopsis thaliana} SCOP: a.4.1.1 Length = 80

 Score = 37.3 bits (86), Expect = 3e-04
 Identities = 18/66 (27%), Positives = 29/66 (43%), Gaps = 4/66 (6%)

Query: 134 GAGNSSPGSGVHSHQRTKRMRTSFKHHQLRTMKSYFNIN----QNPDAKDLKQLAQKTGL 189
           G+  SS  S        KR RT F   Q   M +         Q  D + +++  Q+TG+
Sbjct: 1   GSSGSSGSSAEAGGGIRKRHRTKFTAEQKERMLALAERIGWRIQRQDDEVIQRFCQETGV 60

Query: 190 SKRVLQ 195
            ++VL+
Sbjct: 61  PRQVLK 66

>1uhs_A HOP, homeodomain only protein; structural genomics, cardiac development, riken structural genomics/proteomics initiative, RSGI, transcription; NMR {Mus musculus} SCOP: a.4.1.1 Length = 72

 Score = 37.0 bits (86), Expect = 3e-04
 Identities = 10/42 (23%), Positives = 22/42 (52%), Gaps = 2/42 (4%)

Query: 154 RTSFKHHQLRTMKSYFN-INQNPDAKDLKQLAQKTGLS-KRV 193
             +    Q+  ++  FN +N++PD   L  +A + GL+ ++ 
Sbjct: 5   AATMTEDQVEILEYNFNKVNKHPDPTTLCLIAAEAGLTEEQT 46

>2h8r_A Hepatocyte nuclear factor 1-beta; trasncription factor, POU, homeo, protein-DNA, human disease; 3.20A {Homo sapiens} Length = 221

 Score = 38.8 bits (89), Expect = 4e-04
 Identities = 13/91 (14%), Positives = 31/91 (34%)

Query: 97  PPSEDINANVMRIPSTTLEMLHSGDLSSSMESLSYESGAGNSSPGSGVHSHQRTKRMRTS 156
                 N  V    + T +      L    E      G G S       ++++ +R R  
Sbjct: 89  EILRQFNQTVQSSGNMTDKSSQDQLLFLFPEFSQQSHGPGQSDDACSEPTNKKMRRNRFK 148

Query: 157 FKHHQLRTMKSYFNINQNPDAKDLKQLAQKT 187
           +     + +   ++  +NP  ++ + L ++ 
Sbjct: 149 WGPASQQILYQAYDRQKNPSKEEREALVEEC 179

>2da4_A Hypothetical protein DKFZP686K21156; homeobox domain, three helices with the DNA binding helix- turn-helix motif, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 80

 Score = 36.9 bits (84), Expect = 5e-04
 Identities = 9/58 (15%), Positives = 22/58 (37%), Gaps = 4/58 (6%)

Query: 143 GVHSHQRTKRMRTSFKHHQLRTMKSYFNINQN----PDAKDLKQLAQKTGLSKRVLQN 196
           G        + RT F    L T+K Y++           + ++ +A +  +   +++ 
Sbjct: 1   GSSGSSGALQDRTQFSDRDLATLKKYWDNGMTSLGSVCREKIEAVATELNVDCEIVRT 58

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221

 Score = 39.1 bits (90), Expect = 6e-04
 Identities = 22/172 (12%), Positives = 46/172 (26%), Gaps = 43/172 (25%)

Query: 62  AEIEQPMSPRPAPWQPTTVQKGRPRKRKLSVDSPTPP------------SEDINANVMRI 109
           AE  +        W+     K      + S++   P                 +     I
Sbjct: 334 AESIRDGLATWDNWKHVNCDKLT-TIIESSLNVLEPAEYRKMFDRLSVFPPSAH-----I 387

Query: 110 PSTTLEML----HSGDLSSSMESLSYESGA-GNSSPGS-GVHSHQ---RTKRMRTSFKHH 160
           P+  L ++       D+   +  L   S         +  + S     + K       H 
Sbjct: 388 PTILLSLIWFDVIKSDVMVVVNKLHKYSLVEKQPKESTISIPSIYLELKVKLENEYALHR 447

Query: 161 QL----RTMKSYFNINQNPDAKD----------LK--QLAQKTGLSKRVLQN 196
            +       K++ + +  P   D          LK  +  ++  L + V  +
Sbjct: 448 SIVDHYNIPKTFDSDDLIPPYLDQYFYSHIGHHLKNIEHPERMTLFRMVFLD 499

>2dmt_A Homeobox protein BARH-like 1; homeobox domain, three helices with the DNA binding helix- turn-helix motif, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 80

 Score = 36.3 bits (84), Expect = 6e-04
 Identities = 17/59 (28%), Positives = 26/59 (44%)

Query: 134 GAGNSSPGSGVHSHQRTKRMRTSFKHHQLRTMKSYFNINQNPDAKDLKQLAQKTGLSKR 192
           G+  SS G      ++ +R RT F   QL  ++  F   +     D   LA+  GLS+ 
Sbjct: 1   GSSGSSGGEPGTKAKKGRRSRTVFTELQLMGLEKRFEKQKYLSTPDRIDLAESLGLSQL 59

>2cor_A Pinch protein; LIM domain, particularly interesting NEW Cys- His protein, LIM and senescent cell antigen-like domains 1, structural genomics; NMR {Homo sapiens} SCOP: g.39.1.3 g.39.1.3 Length = 79

 Score = 36.3 bits (84), Expect = 7e-04
 Identities = 10/43 (23%), Positives = 18/43 (41%), Gaps = 2/43 (4%)

Query: 9  VMRARDLVFHLHCFTCISCGILLTKGDLFGMRDEMIYCRPHYE 51
           +  ++  +H   F C +CG  LT           +YC P ++
Sbjct: 29 PLIFKNDPYHPDHFNCANCGKELT--ADARELKGELYCLPCHD 69

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	196
2rgt_A	169	Fusion of LIM/homeobox protein LHX3, linker, INSU	99.38
1wi3_A	71	DNA-binding protein SATB2; homeodomain, helix-turn	99.29
2dmt_A	80	Homeobox protein BARH-like 1; homeobox domain, thr	99.25
1wh5_A	80	ZF-HD homeobox family protein; structural genomics	99.25
1wh7_A	80	ZF-HD homeobox family protein; homeobox domain, st	99.23
2da3_A	80	Alpha-fetoprotein enhancer binding protein; homeob	99.23
2cra_A	70	Homeobox protein HOX-B13; DNA-binding, transcripti	99.16
2djn_A	70	Homeobox protein DLX-5; structural genomics, NPPSF	99.15
2kt0_A	84	Nanog, homeobox protein nanog; homeodomain, struct	99.15
2da1_A	70	Alpha-fetoprotein enhancer binding protein; homeob	99.13
2dmu_A	70	Homeobox protein goosecoid; homeobox domain, three	99.13
2da2_A	70	Alpha-fetoprotein enhancer binding protein; homeob	99.12
2dms_A	80	Homeobox protein OTX2; homeobox domain, three heli	99.1
2cue_A	80	Paired box protein PAX6; homeobox domain, transcri	99.09
1akh_A	61	Protein (mating-type protein A-1); complex (TWO DN	99.09
3f6q_B	72	LIM and senescent cell antigen-like-containing dom	99.09
1nk2_P	77	Homeobox protein VND; homeodomain, DNA-binding pro	99.08
2dmq_A	80	LIM/homeobox protein LHX9; homeobox domain, three	99.08
1puf_A	77	HOX-1.7, homeobox protein HOX-A9; homeodomian, pro	99.08
2l3k_A	123	Rhombotin-2, linker, LIM domain-binding protein 1;	99.07
2hdd_A	61	Protein (engrailed homeodomain Q50K); DNA binding,	99.07
2vi6_A	62	Homeobox protein nanog; homeodomain, DNA-binding,	99.06
1bw5_A	66	ISL-1HD, insulin gene enhancer protein ISL-1; DNA-	99.06
2e1o_A	70	Homeobox protein PRH; DNA binding protein, structu	99.05
2h1k_A	63	IPF-1, pancreatic and duodenal homeobox 1, homeodo	99.04
2da4_A	80	Hypothetical protein DKFZP686K21156; homeobox doma	99.04
2m0c_A	75	Homeobox protein aristaless-like 4; structural gen	99.03
1x61_A	72	Thyroid receptor interacting protein 6; LIM domain	99.03
2l7z_A	73	Homeobox protein HOX-A13; gene regulation; NMR {Ho	99.02
1ig7_A	58	Homeotic protein MSX-1; helix-turn-helix, transcri	99.02
1g47_A	77	Pinch protein; LIM domain, Zn finger, cell adhesio	99.02
1wyh_A	72	SLIM 2, skeletal muscle LIM-protein 2; structural	99.02
1x4k_A	72	Skeletal muscle LIM-protein 3; LIM domain, structu	99.01
1zq3_P	68	PRD-4, homeotic bicoid protein; protein-DNA comple	99.01
1jgg_A	60	Segmentation protein EVEN-skipped; homeodomain, pr	99.0
1ahd_P	68	Antennapedia protein mutant; DNA binding protein/D	98.99
2r5y_A	88	Homeotic protein sex combs reduced; homeodomain; H	98.99
1fjl_A	81	Paired protein; DNA-binding protein, paired BOX, t	98.99
3rkq_A	58	Homeobox protein NKX-2.5; helix-turn-helix, DNA bi	98.98
1b8i_A	81	Ultrabithorax, protein (ultrabithorax homeotic pro	98.97
2ehe_A	82	Four and A half LIM domains 3; FHL-3, skeletal mus	98.97
1yz8_P	68	Pituitary homeobox 2; DNA binding protein, transcr	98.97
3nar_A	96	ZHX1, zinc fingers and homeoboxes protein 1; corep	98.97
1x4l_A	72	Skeletal muscle LIM-protein 3; LIM domain, structu	98.96
1ftt_A	68	TTF-1 HD, thyroid transcription factor 1 homeodoma	98.96
1x63_A	82	Skeletal muscle LIM-protein 1; LIM domain, four an	98.95
2co8_A	82	NEDD9 interacting protein with calponin homology a	98.95
2k40_A	67	Homeobox expressed in ES cells 1; thermostable hom	98.95
1nyp_A	66	Pinch protein; LIM domain, protein recognition, ce	98.95
1x68_A	76	FHL5 protein; four-and-A-half LIM protein 5, zinc	98.94
1x2n_A	73	Homeobox protein pknox1; homeobox domain, structur	98.93
3a01_A	93	Homeodomain-containing protein; homeodomain, prote	98.93
2dn0_A	76	Zinc fingers and homeoboxes protein 3; triple home	98.92
2ecc_A	76	Homeobox and leucine zipper protein homez; homeobo	98.91
1wig_A	73	KIAA1808 protein; LIM domain, zinc finger, metal-b	98.9
1x6a_A	81	LIMK-2, LIM domain kinase 2; LIM-kinase 2, zinc fi	98.9
1x62_A	79	C-terminal LIM domain protein 1; PDZ and LIM domai	98.9
1b72_A	97	Protein (homeobox protein HOX-B1); homeodomain, DN	98.9
1x64_A	89	Alpha-actinin-2 associated LIM protein; LIM domain	98.88
2ly9_A	74	Zinc fingers and homeoboxes protein 1; structural	98.88
2d8x_A	70	Protein pinch; LIM domain, pinch protein, structur	98.88
2cur_A	69	Skeletal muscle LIM-protein 1; four and A half LIM	98.87
2cuf_A	95	FLJ21616 protein; homeobox domain, hepatocyte tran	98.87
2xjy_A	131	Rhombotin-2; oncoprotein, T-cell leukemia, proto-o	98.86
2cu8_A	76	Cysteine-rich protein 2; CRP2, CRIP2, ESP1 protein	98.85
3a02_A	60	Homeobox protein aristaless; homeodomain, developm	98.85
2d8z_A	70	Four and A half LIM domains 2; skeletal muscle LIM	98.85
2hi3_A	73	Homeodomain-only protein; transcription; NMR {Mus	98.84
2egq_A	77	FHL1 protein; LIM domain, four and A half LIM doma	98.84
1du6_A	64	PBX1, homeobox protein PBX1; homeodomain, gene reg	98.84
2l4z_A	123	DNA endonuclease RBBP8, LIM domain transcription L	98.84
2da6_A	102	Hepatocyte nuclear factor 1-beta; homeobox domain,	98.84
1lfb_A	99	Liver transcription factor (LFB1); transcription r	98.83
2dar_A	90	PDZ and LIM domain protein 5; enigma homolog prote	98.83
2d8y_A	91	Eplin protein; LIM domain, epithelial protein LOST	98.82
1a7i_A	81	QCRP2 (LIM1); LIM domain containing proteins, meta	98.81
2dmn_A	83	Homeobox protein TGIF2LX; TGFB-induced factor 2-li	98.8
1uhs_A	72	HOP, homeodomain only protein; structural genomics	98.8
2dj7_A	80	Actin-binding LIM protein 3; LIM domain, Zn bindin	98.79
1puf_B	73	PRE-B-cell leukemia transcription factor-1; homeod	98.79
2cuq_A	80	Four and A half LIM domains 3; structural genomics	98.78
2cor_A	79	Pinch protein; LIM domain, particularly interestin	98.78
2da5_A	75	Zinc fingers and homeoboxes protein 3; homeobox do	98.77
3a03_A	56	T-cell leukemia homeobox protein 2; homeodomain, d	98.76
1iml_A	76	CRIP, cysteine rich intestinal protein; metal-bind	98.76
2iyb_E	65	Testin, TESS, TES; LIM domain, SH3-binding, tumour	98.75
1e3o_C	160	Octamer-binding transcription factor 1; transcript	98.75
1au7_A	146	Protein PIT-1, GHF-1; complex (DNA-binding protein	98.75
2cup_A	101	Skeletal muscle LIM-protein 1; four and half LIM d	98.75
3d1n_I	151	POU domain, class 6, transcription factor 1; prote	98.74
2dlo_A	81	Thyroid receptor-interacting protein 6; LIM domain	98.74
1b72_B	87	Protein (PBX1); homeodomain, DNA, complex, DNA-bin	98.74
1x3h_A	80	Leupaxin; paxillin family, protein-protein interac	98.74
1rut_X	188	Flinc4, fusion protein of LMO4 protein and LIM dom	98.73
1j2o_A	114	FLIN2, fusion of rhombotin-2 and LIM domain-bindin	98.73
1mnm_C	87	Protein (MAT alpha-2 transcriptional repressor); t	98.73
2xsd_C	164	POU domain, class 3, transcription factor 1; trans	98.72
1v6g_A	81	Actin binding LIM protein 2; LIM domain, zinc bind	98.67
2d5v_A	164	Hepatocyte nuclear factor 6; transcription factor,	98.67
1k61_A	60	Mating-type protein alpha-2; protein-DNA complex,	98.66
1m3v_A	122	FLIN4, fusion of the LIM interacting domain of LDB	98.65
3l1p_A	155	POU domain, class 5, transcription factor 1; POU,	98.63
2xqn_T	126	Testin, TESS; metal-binding protein, cytoskeleton,	98.6
1le8_B	83	Mating-type protein alpha-2; matalpha2, isothermal	98.57
2cqx_A	72	LAG1 longevity assurance homolog 5; homeodomain, D	98.56
2xqn_T	126	Testin, TESS; metal-binding protein, cytoskeleton,	98.56
2ecb_A	89	Zinc fingers and homeoboxes protein 1; homeobox do	98.54
3nau_A	66	Zinc fingers and homeoboxes protein 2; ZHX2, corep	98.54
2dmp_A	89	Zinc fingers and homeoboxes protein 2; homeobox do	98.53
2xjy_A	131	Rhombotin-2; oncoprotein, T-cell leukemia, proto-o	98.52
2e19_A	64	Transcription factor 8; homeobox domain, structura	98.46
1rut_X	188	Flinc4, fusion protein of LMO4 protein and LIM dom	98.45
1ic8_A	194	Hepatocyte nuclear factor 1-alpha; transcription r	98.44
2h8r_A	221	Hepatocyte nuclear factor 1-beta; trasncription fa	98.44
1b8t_A	192	Protein (CRP1); LIM domain, muscle differentiation	98.43
2l9r_A	69	Homeobox protein NKX-3.1; structural genomics, nor	98.4
1b8t_A	192	Protein (CRP1); LIM domain, muscle differentiation	98.29
1x2m_A	64	LAG1 longevity assurance homolog 6; homeobox domai	98.25
2rgt_A	169	Fusion of LIM/homeobox protein LHX3, linker, INSU	98.25
2jtn_A	182	LIM domain-binding protein 1, LIM/homeobox protein	98.24
3k2a_A	67	Homeobox protein MEIS2; homeobox domain, DNA-bindi	98.16
2da7_A	71	Zinc finger homeobox protein 1B; homeobox domain,	98.14
1mh3_A	421	Maltose binding-A1 homeodomain protein chimera; MA	97.84
2lk2_A	89	Homeobox protein TGIF1; NESG, structural genomics,	97.53
1j2o_A	114	FLIN2, fusion of rhombotin-2 and LIM domain-bindin	93.11
1m3v_A	122	FLIN4, fusion of the LIM interacting domain of LDB	92.67
1zfo_A	31	LAsp-1; LIM domain, zinc-finger, metal-binding pro	81.44

>2rgt_A Fusion of LIM/homeobox protein LHX3, linker, INSU enhancer protein ISL-1; protein-protein complex, LIM domain, Zn finger, activator, D binding; 2.05A {Mus musculus} PDB: 3mmk_A

Probab=99.38  E-value=6.8e-15  Score=114.64  Aligned_cols=53  Identities=43%  Similarity=0.943  Sum_probs=46.0

Q ss_pred             CCChHHHHHHHHhHHHhhhhhhhhhhcceeccCCccc-cccceeeeccchhhhh
Q psy17504          2 GISSSELVMRARDLVFHLHCFTCISCGILLTKGDLFG-MRDEMIYCRPHYEILR   54 (196)
Q Consensus         2 ~i~~~~~v~~a~~~~~H~~CF~C~~C~~~L~~G~~f~-~~~~~~~C~~~y~~~~   54 (196)
                      .|.+.++|++|.+..||..||+|..|+++|..|+.|+ +.++++||+.||..++
T Consensus        74 ~I~~~~~v~~a~~~~~H~~CF~C~~C~~~L~~g~~f~~~~~g~~~C~~c~~~~~  127 (169)
T 2rgt_A           74 GIPPTQVVRRAQDFVYHLHCFACVVCKRQLATGDEFYLMEDSRLVCKADYETAK  127 (169)
T ss_dssp             BCCTTSEEEEETTEEEEGGGCBCTTTCCBCCTTCEEEECTTSCEEEHHHHHHHH
T ss_pred             ccCCCcEEEEcCCceEeeCCCcCCCCCCCCCCCCceEEccCCeEECHHHHHHHh
Confidence            4666677888999999999999999999997788875 4689999999998765

>1wi3_A DNA-binding protein SATB2; homeodomain, helix-turn-helix, riken structural genomics/proteomics initiative, RSGI, structural genomics; NMR {Homo sapiens} SCOP: a.4.1.1

Probab=99.29  E-value=1.2e-12  Score=86.37  Aligned_cols=49  Identities=20%  Similarity=0.324  Sum_probs=46.4

Q ss_pred             ccccchhhcccchhhHhhhhhhhcc-cCCCChHHHHHHHHHhCcchhhhc
Q psy17504        147 HQRTKRMRTSFKHHQLRTMKSYFNI-NQNPDAKDLKQLAQKTGLSKRVLQ  195 (196)
Q Consensus       147 ~~k~rR~RT~ft~~Ql~~L~~~F~~-~~~p~~~~r~~La~~lgL~~~~Vq  195 (196)
                      .+++||.||.|+.+||..|+..|+. ++||+..+|+.||+.|||++++||
T Consensus         4 ~~~~kR~RT~~s~eQL~~Lqs~f~~~~~yPd~~~r~~La~~tGL~~~~Iq   53 (71)
T 1wi3_A            4 GSSGPRSRTKISLEALGILQSFIHDVGLYPDQEAIHTLSAQLDLPKHTII   53 (71)
T ss_dssp             CCCCCCCCCCCCSHHHHHHHHHHHHHCSCCCHHHHHHHHHHSCCCHHHHH
T ss_pred             CCCCCCCCccCCHHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCHHHHH
Confidence            3467889999999999999999999 999999999999999999999997

>2dmt_A Homeobox protein BARH-like 1; homeobox domain, three helices with the DNA binding helix- turn-helix motif, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.25  E-value=5.4e-12  Score=86.66  Aligned_cols=50  Identities=26%  Similarity=0.357  Sum_probs=47.3

Q ss_pred             cccccchhhcccchhhHhhhhhhhcccCCCChHHHHHHHHHhCcchhhhc
Q psy17504        146 SHQRTKRMRTSFKHHQLRTMKSYFNINQNPDAKDLKQLAQKTGLSKRVLQ  195 (196)
Q Consensus       146 ~~~k~rR~RT~ft~~Ql~~L~~~F~~~~~p~~~~r~~La~~lgL~~~~Vq  195 (196)
                      ..++.||.||.||..|+..|+..|..++||+...+++||..++|++.+||
T Consensus        13 ~~~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~L~~~qV~   62 (80)
T 2dmt_A           13 KAKKGRRSRTVFTELQLMGLEKRFEKQKYLSTPDRIDLAESLGLSQLQVK   62 (80)
T ss_dssp             CCCCCCCSCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHCCCHHHHH
T ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCHHHee
Confidence            45677889999999999999999999999999999999999999999997

>1wh5_A ZF-HD homeobox family protein; structural genomics, zinc finger homeobox family protein, riken structural genomics/proteomics initiative; NMR {Arabidopsis thaliana} SCOP: a.4.1.1

Probab=99.25  E-value=5e-12  Score=86.99  Aligned_cols=49  Identities=29%  Similarity=0.377  Sum_probs=46.3

Q ss_pred             ccccchhhcccchhhHhhhhhhhcc----cCCCChHHHHHHHHHhCcchhhhc
Q psy17504        147 HQRTKRMRTSFKHHQLRTMKSYFNI----NQNPDAKDLKQLAQKTGLSKRVLQ  195 (196)
Q Consensus       147 ~~k~rR~RT~ft~~Ql~~L~~~F~~----~~~p~~~~r~~La~~lgL~~~~Vq  195 (196)
                      .++.||.||.||..|+.+|+..|+.    ++||+...|++||..|||++++||
T Consensus        14 ~~~~rR~Rt~ft~~Ql~~Le~~f~~~~~~~~yp~~~~r~~La~~lgL~~~~Vk   66 (80)
T 1wh5_A           14 GGIRKRHRTKFTAEQKERMLALAERIGWRIQRQDDEVIQRFCQETGVPRQVLK   66 (80)
T ss_dssp             CCCSCCCSCCCCHHHHHHHHHHHHHHTSCCCTTTHHHHHHHHHHSCCCHHHHH
T ss_pred             CCCCCCCCccCCHHHHHHHHHHHHhccCcCCCcCHHHHHHHHHHhCCCccccc
Confidence            3567889999999999999999999    999999999999999999999997

>1wh7_A ZF-HD homeobox family protein; homeobox domain, structural genomics, riken structural genomics/proteomics initiative, RSGI; NMR {Arabidopsis thaliana} SCOP: a.4.1.1

Probab=99.23  E-value=6.5e-12  Score=86.40  Aligned_cols=49  Identities=35%  Similarity=0.448  Sum_probs=45.5

Q ss_pred             cccccchhhcccchhhHhhhhhhhcc-----cCCCChHHHHHHHHHhCcchhhhc
Q psy17504        146 SHQRTKRMRTSFKHHQLRTMKSYFNI-----NQNPDAKDLKQLAQKTGLSKRVLQ  195 (196)
Q Consensus       146 ~~~k~rR~RT~ft~~Ql~~L~~~F~~-----~~~p~~~~r~~La~~lgL~~~~Vq  195 (196)
                      ...+.||.||.||..|+..|+ .|..     ++||+...|++||..|+|++++||
T Consensus        13 ~~~~~rR~Rt~ft~~Ql~~Le-~F~~~~~w~~~yp~~~~r~~La~~lgL~e~qVk   66 (80)
T 1wh7_A           13 SGGTTKRFRTKFTAEQKEKML-AFAERLGWRIQKHDDVAVEQFCAETGVRRQVLK   66 (80)
T ss_dssp             CCCCSSCCCCCCCHHHHHHHH-HHHHHHTSCCCSSTTHHHHHHHHHSCCCHHHHH
T ss_pred             CCCCCCCCCccCCHHHHHHHH-HHHHHcCcCCCCCCHHHHHHHHHHhCcCcCccc
Confidence            345678899999999999999 8999     999999999999999999999997

>2da3_A Alpha-fetoprotein enhancer binding protein; homeobox domain, three helices with the DNA binding helix- turn-helix motif, structural genomics; NMR {Homo sapiens}

Probab=99.23  E-value=7.5e-12  Score=85.74  Aligned_cols=50  Identities=38%  Similarity=0.599  Sum_probs=47.0

Q ss_pred             cccccchhhcccchhhHhhhhhhhcccCCCChHHHHHHHHHhCcchhhhc
Q psy17504        146 SHQRTKRMRTSFKHHQLRTMKSYFNINQNPDAKDLKQLAQKTGLSKRVLQ  195 (196)
Q Consensus       146 ~~~k~rR~RT~ft~~Ql~~L~~~F~~~~~p~~~~r~~La~~lgL~~~~Vq  195 (196)
                      ..++.||.||.||..|+..|+..|..++||+...+++||..+||++.+||
T Consensus        13 ~~~~~rr~Rt~ft~~Ql~~Le~~f~~~~yp~~~~r~~La~~l~l~~~qV~   62 (80)
T 2da3_A           13 EPQRDKRLRTTITPEQLEILYQKYLLDSNPTRKMLDHIAHEVGLKKRVVQ   62 (80)
T ss_dssp             CCCCCTTCCSSCCTTTHHHHHHHHHHCSSCCHHHHHHHHHHHTSCHHHHH
T ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHHCcCHHHhH
Confidence            44577889999999999999999999999999999999999999999997

>2cra_A Homeobox protein HOX-B13; DNA-binding, transcription regulation, helix-turn-helix, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: a.4.1.1

Probab=99.16  E-value=1.7e-11  Score=82.07  Aligned_cols=49  Identities=18%  Similarity=0.332  Sum_probs=46.0

Q ss_pred             ccccchhhcccchhhHhhhhhhhcccCCCChHHHHHHHHHhCcchhhhc
Q psy17504        147 HQRTKRMRTSFKHHQLRTMKSYFNINQNPDAKDLKQLAQKTGLSKRVLQ  195 (196)
Q Consensus       147 ~~k~rR~RT~ft~~Ql~~L~~~F~~~~~p~~~~r~~La~~lgL~~~~Vq  195 (196)
                      ..+.||.||.||..|+..|+..|..++||+...+++||..+||++.+||
T Consensus         4 ~~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~   52 (70)
T 2cra_A            4 GSSGRKKRIPYSKGQLRELEREYAANKFITKDKRRKISAATSLSERQIT   52 (70)
T ss_dssp             SCCCCCSCCCSCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTCCCHHHHH
T ss_pred             CCCCCCCCCcCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHHCCCHHHhh
Confidence            3466789999999999999999999999999999999999999999997

>2djn_A Homeobox protein DLX-5; structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.15  E-value=2.1e-11  Score=81.57  Aligned_cols=48  Identities=21%  Similarity=0.322  Sum_probs=45.7

Q ss_pred             cccchhhcccchhhHhhhhhhhcccCCCChHHHHHHHHHhCcchhhhc
Q psy17504        148 QRTKRMRTSFKHHQLRTMKSYFNINQNPDAKDLKQLAQKTGLSKRVLQ  195 (196)
Q Consensus       148 ~k~rR~RT~ft~~Ql~~L~~~F~~~~~p~~~~r~~La~~lgL~~~~Vq  195 (196)
                      .+.||.||.||..|+..|+..|..++||+...+++||..+||++.+||
T Consensus         5 ~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~   52 (70)
T 2djn_A            5 SSGRKPRTIYSSFQLAALQRRFQKTQYLALPERAELAASLGLTQTQVK   52 (70)
T ss_dssp             CCCCCSSCSSCHHHHHHHHHHHTTCSSCCHHHHHHHHHHSSCCHHHHH
T ss_pred             CCCCCCCCCCCHHHHHHHHHHHcCCCCCCHHHHHHHHHHhCCCHHHHH
Confidence            466889999999999999999999999999999999999999999997

>2kt0_A Nanog, homeobox protein nanog; homeodomain, structural genomics, protein structure initiative, PSI, center for eukaryotic structural genomics; NMR {Homo sapiens}

Probab=99.15  E-value=3.5e-11  Score=83.17  Aligned_cols=50  Identities=18%  Similarity=0.303  Sum_probs=46.8

Q ss_pred             cccccchhhcccchhhHhhhhhhhcccCCCChHHHHHHHHHhCcchhhhc
Q psy17504        146 SHQRTKRMRTSFKHHQLRTMKSYFNINQNPDAKDLKQLAQKTGLSKRVLQ  195 (196)
Q Consensus       146 ~~~k~rR~RT~ft~~Ql~~L~~~F~~~~~p~~~~r~~La~~lgL~~~~Vq  195 (196)
                      ...+.||.||.|+..|+..|+..|..++||+...+++||..+||++.+||
T Consensus        18 ~~~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~   67 (84)
T 2kt0_A           18 VPVKKQKTRTVFSSTQLCVLNDRFQRQKYLSLQQMQELSNILNLSYKQVK   67 (84)
T ss_dssp             CCSCSCCCSSCCCHHHHHHHHHHHHHSSSCCHHHHHHHHHHTTCCHHHHH
T ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCCHHHHH
Confidence            34567889999999999999999999999999999999999999999997

>2da1_A Alpha-fetoprotein enhancer binding protein; homeobox domain, three helices with the DNA binding helix- turn-helix motif, structural genomics; NMR {Homo sapiens}

Probab=99.13  E-value=2.2e-11  Score=81.35  Aligned_cols=49  Identities=37%  Similarity=0.728  Sum_probs=46.2

Q ss_pred             ccccchhhcccchhhHhhhhhhhcccCCCChHHHHHHHHHhCcchhhhc
Q psy17504        147 HQRTKRMRTSFKHHQLRTMKSYFNINQNPDAKDLKQLAQKTGLSKRVLQ  195 (196)
Q Consensus       147 ~~k~rR~RT~ft~~Ql~~L~~~F~~~~~p~~~~r~~La~~lgL~~~~Vq  195 (196)
                      ..+.||.||.||..|+..|+..|+.++||+...+++||..+||++.+|+
T Consensus         4 ~~~~rr~Rt~ft~~q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~   52 (70)
T 2da1_A            4 GSSGKRPRTRITDDQLRVLRQYFDINNSPSEEQIKEMADKSGLPQKVIK   52 (70)
T ss_dssp             SCCCCSCSCCCCHHHHHHHHHHHHHCSSCCTTHHHHHHHHHCCCHHHHH
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHhCCCHHHHH
Confidence            3467889999999999999999999999999999999999999999997

>2dmu_A Homeobox protein goosecoid; homeobox domain, three helices with the DNA binding helix- turn-helix motif, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.13  E-value=2.5e-11  Score=81.11  Aligned_cols=48  Identities=29%  Similarity=0.462  Sum_probs=45.4

Q ss_pred             cccchhhcccchhhHhhhhhhhcccCCCChHHHHHHHHHhCcchhhhc
Q psy17504        148 QRTKRMRTSFKHHQLRTMKSYFNINQNPDAKDLKQLAQKTGLSKRVLQ  195 (196)
Q Consensus       148 ~k~rR~RT~ft~~Ql~~L~~~F~~~~~p~~~~r~~La~~lgL~~~~Vq  195 (196)
                      .+.||.||.||..|+..|+..|..++||+...+++||..+||++.+|+
T Consensus         5 ~~~rr~Rt~ft~~q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~   52 (70)
T 2dmu_A            5 SSGRRHRTIFTDEQLEALENLFQETKYPDVGTREQLARKVHLREEKVE   52 (70)
T ss_dssp             TSSCCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHH
T ss_pred             CCCCCCCCCCCHHHHHHHHHHHHccCCCCHHHHHHHHHHHCCCHHHee
Confidence            356788999999999999999999999999999999999999999997

>2da2_A Alpha-fetoprotein enhancer binding protein; homeobox domain, three helices with the DNA binding helix- turn-helix motif, structural genomics; NMR {Homo sapiens}

Probab=99.12  E-value=2.7e-11  Score=80.92  Aligned_cols=49  Identities=29%  Similarity=0.520  Sum_probs=46.0

Q ss_pred             ccccchhhcccchhhHhhhhhhhcccCCCChHHHHHHHHHhCcchhhhc
Q psy17504        147 HQRTKRMRTSFKHHQLRTMKSYFNINQNPDAKDLKQLAQKTGLSKRVLQ  195 (196)
Q Consensus       147 ~~k~rR~RT~ft~~Ql~~L~~~F~~~~~p~~~~r~~La~~lgL~~~~Vq  195 (196)
                      ..+.||.||.|+..|+..|+..|..++||+...+++||..+||++.+|+
T Consensus         4 ~~~~rr~Rt~ft~~q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~   52 (70)
T 2da2_A            4 GSSGRSSRTRFTDYQLRVLQDFFDANAYPKDDEFEQLSNLLNLPTRVIV   52 (70)
T ss_dssp             SCCSCCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHSCCCHHHHH
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHcCCCcCHHHHHHHHHHhCCCHHHhH
Confidence            3466789999999999999999999999999999999999999999997

>2dms_A Homeobox protein OTX2; homeobox domain, three helices with the DNA binding helix- turn-helix motif, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=99.10  E-value=4.2e-11  Score=82.11  Aligned_cols=49  Identities=27%  Similarity=0.373  Sum_probs=46.2

Q ss_pred             ccccchhhcccchhhHhhhhhhhcccCCCChHHHHHHHHHhCcchhhhc
Q psy17504        147 HQRTKRMRTSFKHHQLRTMKSYFNINQNPDAKDLKQLAQKTGLSKRVLQ  195 (196)
Q Consensus       147 ~~k~rR~RT~ft~~Ql~~L~~~F~~~~~p~~~~r~~La~~lgL~~~~Vq  195 (196)
                      .++.||.||.|+..|+..|+..|..++||+...+++||..++|++.+|+
T Consensus         4 ~~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~   52 (80)
T 2dms_A            4 GSSGRRERTTFTRAQLDVLEALFAKTRYPDIFMREEVALKINLPESRVQ   52 (80)
T ss_dssp             CCCCCCCCSSCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTTCCHHHHH
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHccCCCCHHHHHHHHHHHCcCHHHhh
Confidence            3467889999999999999999999999999999999999999999997

>2cue_A Paired box protein PAX6; homeobox domain, transcription factor, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: a.4.1.1

Probab=99.09  E-value=5.9e-11  Score=81.41  Aligned_cols=48  Identities=29%  Similarity=0.427  Sum_probs=45.5

Q ss_pred             cccchhhcccchhhHhhhhhhhcccCCCChHHHHHHHHHhCcchhhhc
Q psy17504        148 QRTKRMRTSFKHHQLRTMKSYFNINQNPDAKDLKQLAQKTGLSKRVLQ  195 (196)
Q Consensus       148 ~k~rR~RT~ft~~Ql~~L~~~F~~~~~p~~~~r~~La~~lgL~~~~Vq  195 (196)
                      .+.||.||.|+..|+..|+..|..++||+...+++||..+||++.+||
T Consensus         5 ~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~   52 (80)
T 2cue_A            5 SSGQRNRTSFTQEQIEALEKEFERTHYPDVFARERLAAKIDLPEARIQ   52 (80)
T ss_dssp             CSSCCCCCCSCHHHHHHHHHHHTTCSSCCHHHHHHHHHHTTCCHHHHH
T ss_pred             CCCCCCCCccCHHHHHHHHHHHhccCCCCHHHHHHHHHHhCCCHHHhh
Confidence            356789999999999999999999999999999999999999999997

>1akh_A Protein (mating-type protein A-1); complex (TWO DNA-binding proteins/DNA), complex, DNA- binding protein, DNA; HET: DNA; 2.50A {Saccharomyces cerevisiae} SCOP: a.4.1.1 PDB: 1f43_A 1yrn_A*

Probab=99.09  E-value=4.8e-11  Score=77.56  Aligned_cols=49  Identities=14%  Similarity=0.295  Sum_probs=38.8

Q ss_pred             cccchhhcccchhhHhhhhhhhcccCCCChHHHHHHHHHhCcchhhhcC
Q psy17504        148 QRTKRMRTSFKHHQLRTMKSYFNINQNPDAKDLKQLAQKTGLSKRVLQN  196 (196)
Q Consensus       148 ~k~rR~RT~ft~~Ql~~L~~~F~~~~~p~~~~r~~La~~lgL~~~~Vq~  196 (196)
                      ++.+|.||.|+..|+..|+..|..++||+...+++||..+||++.+|++
T Consensus         3 ~k~rr~Rt~ft~~q~~~Le~~f~~~~yp~~~~r~~La~~~~l~~~qV~~   51 (61)
T 1akh_A            3 EKSPKGKSSISPQARAFLEEVFRRKQSLNSKEKEEVAKKCGITPLQVRV   51 (61)
T ss_dssp             ---------CCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTSCHHHHHH
T ss_pred             CCCCCCCCCCCHHHHHHHHHHHHhCCCcCHHHHHHHHHHHCcCHHHHHH
Confidence            4678899999999999999999999999999999999999999999973

>3f6q_B LIM and senescent cell antigen-like-containing domain protein 1; ILK, integrin-linked kinase, pinch, ankyrin repeat, ANK, IPP; 1.60A {Homo sapiens} PDB: 2kbx_B 3ixe_B

Probab=99.09  E-value=1.4e-12  Score=86.99  Aligned_cols=52  Identities=25%  Similarity=0.627  Sum_probs=45.6

Q ss_pred             CCChHHHHHHHHhHHHhhhhhhhhhhcceeccCCccccccceeeeccchhhhh
Q psy17504          2 GISSSELVMRARDLVFHLHCFTCISCGILLTKGDLFGMRDEMIYCRPHYEILR   54 (196)
Q Consensus         2 ~i~~~~~v~~a~~~~~H~~CF~C~~C~~~L~~G~~f~~~~~~~~C~~~y~~~~   54 (196)
                      .|.+.+.++++.++.||..||+|..|+++|..+ .|...++++||+.||..+|
T Consensus        20 ~i~~~e~~~~~~~~~~H~~CF~C~~C~~~L~~~-~~~~~~g~~yC~~~y~~lf   71 (72)
T 3f6q_B           20 GFAPAEKIVNSNGELYHEQCFVCAQCFQQFPEG-LFYEFEGRKYCEHDFQMLF   71 (72)
T ss_dssp             BCCTTCEEEEETTEEEETTTSSCTTTCCCCGGG-CCEEETTEEECHHHHHHHT
T ss_pred             cccCCceEEEeCcCeeCcCCCcccCCCCCCCCC-CeEeECCeEeCHHHHHHhh
Confidence            456667778899999999999999999999665 7778899999999999876

>1nk2_P Homeobox protein VND; homeodomain, DNA-binding protein, embryonic development, complex (homeodomain/DNA); HET: DNA; NMR {Drosophila melanogaster} SCOP: a.4.1.1 PDB: 1nk3_P* 1vnd_A 1qry_A

Probab=99.08  E-value=5.8e-11  Score=80.85  Aligned_cols=49  Identities=16%  Similarity=0.244  Sum_probs=46.0

Q ss_pred             ccccchhhcccchhhHhhhhhhhcccCCCChHHHHHHHHHhCcchhhhc
Q psy17504        147 HQRTKRMRTSFKHHQLRTMKSYFNINQNPDAKDLKQLAQKTGLSKRVLQ  195 (196)
Q Consensus       147 ~~k~rR~RT~ft~~Ql~~L~~~F~~~~~p~~~~r~~La~~lgL~~~~Vq  195 (196)
                      .++.||.||.||..|+..|+..|..++||+...+++||..+||++.+||
T Consensus         6 ~~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~   54 (77)
T 1nk2_P            6 PNKKRKRRVLFTKAQTYELERRFRQQRYLSAPEREHLASLIRLTPTQVK   54 (77)
T ss_dssp             SCCCCCCCCCCCHHHHHHHHHHHHHCSCCCHHHHHHHHHHTTCCHHHHH
T ss_pred             CCCCCCCCccCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCHHHHH
Confidence            3466788999999999999999999999999999999999999999997

>2dmq_A LIM/homeobox protein LHX9; homeobox domain, three helices with the DNA binding helix- turn-helix motif, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.08  E-value=5.9e-11  Score=81.29  Aligned_cols=48  Identities=88%  Similarity=1.186  Sum_probs=45.6

Q ss_pred             cccchhhcccchhhHhhhhhhhcccCCCChHHHHHHHHHhCcchhhhc
Q psy17504        148 QRTKRMRTSFKHHQLRTMKSYFNINQNPDAKDLKQLAQKTGLSKRVLQ  195 (196)
Q Consensus       148 ~k~rR~RT~ft~~Ql~~L~~~F~~~~~p~~~~r~~La~~lgL~~~~Vq  195 (196)
                      .+.||.||.||..|+..|+..|..++||+...+++||..+||++.+|+
T Consensus         5 ~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~   52 (80)
T 2dmq_A            5 SSGKRMRTSFKHHQLRTMKSYFAINHNPDAKDLKQLAQKTGLTKRVLQ   52 (80)
T ss_dssp             CCCCCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTCCCHHHHH
T ss_pred             CCCCCCCCCCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHhCCCHHHhh
Confidence            356789999999999999999999999999999999999999999997

>1puf_A HOX-1.7, homeobox protein HOX-A9; homeodomian, protein-DNA complex, HOX hexapeptide, TALE homeodomain, homeodomain interaction; 1.90A {Mus musculus} SCOP: a.4.1.1 PDB: 1san_A

Probab=99.08  E-value=8.2e-11  Score=80.10  Aligned_cols=49  Identities=18%  Similarity=0.280  Sum_probs=46.2

Q ss_pred             ccccchhhcccchhhHhhhhhhhcccCCCChHHHHHHHHHhCcchhhhc
Q psy17504        147 HQRTKRMRTSFKHHQLRTMKSYFNINQNPDAKDLKQLAQKTGLSKRVLQ  195 (196)
Q Consensus       147 ~~k~rR~RT~ft~~Ql~~L~~~F~~~~~p~~~~r~~La~~lgL~~~~Vq  195 (196)
                      .++.+|.||.||..|+..|+..|..++||+...+++||..+||++.+||
T Consensus        10 ~~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~   58 (77)
T 1puf_A           10 ARSTRKKRCPYTKHQTLELEKEFLFNMYLTRDRRYEVARLLNLTERQVK   58 (77)
T ss_dssp             CCTTSCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHH
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHhccCCCCHHHHHHHHHHHCcCHHHHH
Confidence            3567789999999999999999999999999999999999999999997

>2hdd_A Protein (engrailed homeodomain Q50K); DNA binding, complex (DNA binding protein/DNA), transcription/DNA complex; HET: DNA; 1.90A {Drosophila melanogaster} SCOP: a.4.1.1 PDB: 1hdd_C* 2jwt_A 3hdd_A 1p7j_A* 1p7i_A* 2hos_A 2hot_A 1du0_A* 1ztr_A 1enh_A 2p81_A

Probab=99.07  E-value=6.3e-11  Score=77.05  Aligned_cols=46  Identities=33%  Similarity=0.466  Sum_probs=41.4

Q ss_pred             cchhhcccchhhHhhhhhhhcccCCCChHHHHHHHHHhCcchhhhc
Q psy17504        150 TKRMRTSFKHHQLRTMKSYFNINQNPDAKDLKQLAQKTGLSKRVLQ  195 (196)
Q Consensus       150 ~rR~RT~ft~~Ql~~L~~~F~~~~~p~~~~r~~La~~lgL~~~~Vq  195 (196)
                      .||.||.||..|+..|+..|..++||+...+++||..+||++.+||
T Consensus         3 ~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~   48 (61)
T 2hdd_A            3 EKRPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIK   48 (61)
T ss_dssp             ----CCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHH
T ss_pred             CCCCCCCCCHHHHHHHHHHHHccCCCCHHHHHHHHHHHCcCHHHHH
Confidence            5789999999999999999999999999999999999999999997

>2vi6_A Homeobox protein nanog; homeodomain, DNA-binding, transcription, transcription facto developmental protein, transcription regulation, NUC homeobox; 2.6A {Mus musculus}

Probab=99.06  E-value=7.2e-11  Score=77.04  Aligned_cols=47  Identities=23%  Similarity=0.388  Sum_probs=40.4

Q ss_pred             ccchhhcccchhhHhhhhhhhcccCCCChHHHHHHHHHhCcchhhhc
Q psy17504        149 RTKRMRTSFKHHQLRTMKSYFNINQNPDAKDLKQLAQKTGLSKRVLQ  195 (196)
Q Consensus       149 k~rR~RT~ft~~Ql~~L~~~F~~~~~p~~~~r~~La~~lgL~~~~Vq  195 (196)
                      +.+|.||.||..|+..|+..|..++||+...+++||..+||++.+|+
T Consensus         2 ~~rr~Rt~ft~~q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~   48 (62)
T 2vi6_A            2 TKQKMRTVFSQAQLCALKDRFQKQKYLSLQQMQELSSILNLSYKQVK   48 (62)
T ss_dssp             ------CCCCHHHHHHHHHHHHHCSCCCHHHHHHHHHHHTCCHHHHH
T ss_pred             CCCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCHHHhh
Confidence            46789999999999999999999999999999999999999999997

>1bw5_A ISL-1HD, insulin gene enhancer protein ISL-1; DNA-binding protein, homeodomain, LIM domain; NMR {Rattus norvegicus} SCOP: a.4.1.1

Probab=99.06  E-value=7.8e-11  Score=77.82  Aligned_cols=47  Identities=40%  Similarity=0.629  Sum_probs=45.0

Q ss_pred             ccchhhcccchhhHhhhhhhhcccCCCChHHHHHHHHHhCcchhhhc
Q psy17504        149 RTKRMRTSFKHHQLRTMKSYFNINQNPDAKDLKQLAQKTGLSKRVLQ  195 (196)
Q Consensus       149 k~rR~RT~ft~~Ql~~L~~~F~~~~~p~~~~r~~La~~lgL~~~~Vq  195 (196)
                      +.||.||.||..|+..|+..|..++||+...+++||..+||++.+|+
T Consensus         2 k~rr~Rt~ft~~q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~   48 (66)
T 1bw5_A            2 KTTRVRTVLNEKQLHTLRTCYAANPRPDALMKEQLVEMTGLSPRVIR   48 (66)
T ss_dssp             CCSCCCCCCSHHHHHHHHHHHHHCSCCCHHHHHHHHHHHTSCHHHHH
T ss_pred             CCCCCCCCCCHHHHHHHHHHHhcCCCcCHHHHHHHHHHHCcCHHHHH
Confidence            46789999999999999999999999999999999999999999997

>2e1o_A Homeobox protein PRH; DNA binding protein, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: a.4.1.1

Probab=99.05  E-value=8.5e-11  Score=78.55  Aligned_cols=47  Identities=21%  Similarity=0.268  Sum_probs=44.6

Q ss_pred             ccchhhcccchhhHhhhhhhhcccCCCChHHHHHHHHHhCcchhhhc
Q psy17504        149 RTKRMRTSFKHHQLRTMKSYFNINQNPDAKDLKQLAQKTGLSKRVLQ  195 (196)
Q Consensus       149 k~rR~RT~ft~~Ql~~L~~~F~~~~~p~~~~r~~La~~lgL~~~~Vq  195 (196)
                      +.++.||.||..|+..|+..|..++||+...+++||..+||++.+|+
T Consensus         6 ~~~r~R~~ft~~q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~   52 (70)
T 2e1o_A            6 SGKGGQVRFSNDQTIELEKKFETQKYLSPPERKRLAKMLQLSERQVK   52 (70)
T ss_dssp             CCCCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTTCCHHHHH
T ss_pred             CCCCCCCCCCHHHHHHHHHHHHcCCCcCHHHHHHHHHHHCCCHHHhh
Confidence            45678999999999999999999999999999999999999999997

>2h1k_A IPF-1, pancreatic and duodenal homeobox 1, homeodomain; protein-DNA complex, transcription/DNA complex; 2.42A {Mesocricetus auratus}

Probab=99.04  E-value=9.2e-11  Score=76.80  Aligned_cols=47  Identities=26%  Similarity=0.328  Sum_probs=43.0

Q ss_pred             ccchhhcccchhhHhhhhhhhcccCCCChHHHHHHHHHhCcchhhhc
Q psy17504        149 RTKRMRTSFKHHQLRTMKSYFNINQNPDAKDLKQLAQKTGLSKRVLQ  195 (196)
Q Consensus       149 k~rR~RT~ft~~Ql~~L~~~F~~~~~p~~~~r~~La~~lgL~~~~Vq  195 (196)
                      +.||.||.||..|+..|+..|..++||+...+++||..+||++.+||
T Consensus         2 ~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~   48 (63)
T 2h1k_A            2 SNKRTRTAYTRAQLLELEKEFLFNKYISRPRRVELAVMLNLTERHIK   48 (63)
T ss_dssp             ---CCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHH
T ss_pred             CCCCCCCCcCHHHHHHHHHHHhcCCCcCHHHHHHHHHHhCcCHHHhh
Confidence            35778999999999999999999999999999999999999999997

>2da4_A Hypothetical protein DKFZP686K21156; homeobox domain, three helices with the DNA binding helix- turn-helix motif, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.04  E-value=5e-11  Score=81.76  Aligned_cols=49  Identities=16%  Similarity=0.316  Sum_probs=46.2

Q ss_pred             ccccchhhcccchhhHhhhhhhhccc----CCCChHHHHHHHHHhCcchhhhc
Q psy17504        147 HQRTKRMRTSFKHHQLRTMKSYFNIN----QNPDAKDLKQLAQKTGLSKRVLQ  195 (196)
Q Consensus       147 ~~k~rR~RT~ft~~Ql~~L~~~F~~~----~~p~~~~r~~La~~lgL~~~~Vq  195 (196)
                      .++.||.||.||..|+..|+..|+.+    +||+...+++||..+||++.+||
T Consensus         5 ~~~~rr~Rt~ft~~Q~~~Le~~F~~~~~~~~yp~~~~r~~La~~lgL~~~qV~   57 (80)
T 2da4_A            5 SSGALQDRTQFSDRDLATLKKYWDNGMTSLGSVCREKIEAVATELNVDCEIVR   57 (80)
T ss_dssp             CCCCCCSSCCCCHHHHHHHHHHHTTTTTCCSHHHHHHHHHHHHHHTCCHHHHH
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHhCCCCCCCcCHHHHHHHHHHhCCCHHHhh
Confidence            34678899999999999999999999    99999999999999999999997

>2m0c_A Homeobox protein aristaless-like 4; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative; NMR {Homo sapiens}

Probab=99.03  E-value=1.3e-10  Score=78.41  Aligned_cols=48  Identities=31%  Similarity=0.468  Sum_probs=45.5

Q ss_pred             cccchhhcccchhhHhhhhhhhcccCCCChHHHHHHHHHhCcchhhhc
Q psy17504        148 QRTKRMRTSFKHHQLRTMKSYFNINQNPDAKDLKQLAQKTGLSKRVLQ  195 (196)
Q Consensus       148 ~k~rR~RT~ft~~Ql~~L~~~F~~~~~p~~~~r~~La~~lgL~~~~Vq  195 (196)
                      .+.+|.||.|+..|+..|+..|..++||+...+++||..+||++.+|+
T Consensus         7 ~~~rr~Rt~ft~~q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~   54 (75)
T 2m0c_A            7 GKKRRNRTTFTSYQLEELEKVFQKTHYPDVYAREQLAMRTDLTEARVQ   54 (75)
T ss_dssp             SCCCSCSCSSCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHH
T ss_pred             CCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCHHHHH
Confidence            466789999999999999999999999999999999999999999996

>1x61_A Thyroid receptor interacting protein 6; LIM domain, OPA-interacting protein 1, zyxin related protein 1 (ZRP-1), structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: g.39.1.3 g.39.1.3

Probab=99.03  E-value=3.9e-12  Score=85.13  Aligned_cols=53  Identities=28%  Similarity=0.546  Sum_probs=46.6

Q ss_pred             CCChHHHHHHHHhHHHhhhhhhhhhhcceeccCCccccccceeeeccchhhhhh
Q psy17504          2 GISSSELVMRARDLVFHLHCFTCISCGILLTKGDLFGMRDEMIYCRPHYEILRH   55 (196)
Q Consensus         2 ~i~~~~~v~~a~~~~~H~~CF~C~~C~~~L~~G~~f~~~~~~~~C~~~y~~~~~   55 (196)
                      .|.+.+.++.|.++.||..||+|..|+++| .+..|+..++++||+.||..++.
T Consensus        14 ~I~~~~~~~~a~~~~~H~~CF~C~~C~~~L-~~~~~~~~~~~~yC~~cy~~~~~   66 (72)
T 1x61_A           14 DVVGDGAGVVALDRVFHVGCFVCSTCRAQL-RGQHFYAVERRAYCEGCYVATLE   66 (72)
T ss_dssp             CCCSSSCCEECSSSEECTTTCBCSSSCCBC-TTSCEEESSSCEEEHHHHHHHHH
T ss_pred             ccCCCceEEEECCCeEcccCCcccccCCcC-CcCcCEeeCCeEECHHHHHHHHc
Confidence            355556678899999999999999999999 67788889999999999998875

>2l7z_A Homeobox protein HOX-A13; gene regulation; NMR {Homo sapiens} PDB: 2ld5_A*

Probab=99.02  E-value=1.3e-10  Score=78.38  Aligned_cols=49  Identities=16%  Similarity=0.309  Sum_probs=46.1

Q ss_pred             ccccchhhcccchhhHhhhhhhhcccCCCChHHHHHHHHHhCcchhhhc
Q psy17504        147 HQRTKRMRTSFKHHQLRTMKSYFNINQNPDAKDLKQLAQKTGLSKRVLQ  195 (196)
Q Consensus       147 ~~k~rR~RT~ft~~Ql~~L~~~F~~~~~p~~~~r~~La~~lgL~~~~Vq  195 (196)
                      ..+.||.||.||..|+..|+..|..++||+...+++||..+||++.+||
T Consensus         4 ~~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~   52 (73)
T 2l7z_A            4 MLEGRKKRVPYTKVQLKELEREYATNKFITKDKRRRISATTNLSERQVT   52 (73)
T ss_dssp             SSCCCCCCCCSCHHHHHHHHHHHHHTSCCCHHHHHHHHHHHTSCSHHHH
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHhhCCCcCHHHHHHHHHHHCCCHHHHH
Confidence            3466889999999999999999999999999999999999999999997

>1ig7_A Homeotic protein MSX-1; helix-turn-helix, transcription/DNA complex; 2.20A {Mus musculus} SCOP: a.4.1.1

Probab=99.02  E-value=1.3e-10  Score=74.72  Aligned_cols=45  Identities=18%  Similarity=0.301  Sum_probs=43.3

Q ss_pred             chhhcccchhhHhhhhhhhcccCCCChHHHHHHHHHhCcchhhhc
Q psy17504        151 KRMRTSFKHHQLRTMKSYFNINQNPDAKDLKQLAQKTGLSKRVLQ  195 (196)
Q Consensus       151 rR~RT~ft~~Ql~~L~~~F~~~~~p~~~~r~~La~~lgL~~~~Vq  195 (196)
                      ||.||.||..|+..|+..|..++||+...+++||..+||++.+||
T Consensus         1 rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~   45 (58)
T 1ig7_A            1 RKPRTPFTTAQLLALERKFRQKQYLSIAERAEFSSSLSLTETQVK   45 (58)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHHCSCCCHHHHHHHHHHTTCCHHHHH
T ss_pred             CCCCCCCCHHHHHHHHHHHhcCCCcCHHHHHHHHHHHCcCHHHhh
Confidence            568999999999999999999999999999999999999999997

>1g47_A Pinch protein; LIM domain, Zn finger, cell adhesion; NMR {Homo sapiens} SCOP: g.39.1.3 g.39.1.3

Probab=99.02  E-value=4.6e-12  Score=85.76  Aligned_cols=53  Identities=25%  Similarity=0.610  Sum_probs=46.3

Q ss_pred             CCChHHHHHHHHhHHHhhhhhhhhhhcceeccCCccccccceeeeccchhhhhh
Q psy17504          2 GISSSELVMRARDLVFHLHCFTCISCGILLTKGDLFGMRDEMIYCRPHYEILRH   55 (196)
Q Consensus         2 ~i~~~~~v~~a~~~~~H~~CF~C~~C~~~L~~G~~f~~~~~~~~C~~~y~~~~~   55 (196)
                      .|.+.+.+++|.++.||..||+|..|+++|..+ .|...++++||+.||..++.
T Consensus        20 ~I~~~~~~~~a~~~~~H~~CF~C~~C~~~L~~~-~~~~~~g~~yC~~~y~~~f~   72 (77)
T 1g47_A           20 GFAPAEKIVNSNGELYHEQCFVCAQCFQQFPEG-LFYEFEGRKYCEHDFQMLFA   72 (77)
T ss_dssp             BCCSTTTCEEETTEEECTTTCCCTTTCCCCGGG-CSEEETTEEECHHHHHHHCC
T ss_pred             ccCCCceEEEeCccEeccccCeECCCCCCCCCC-CeEeECCeEeCHHHHHHHhh
Confidence            456677888999999999999999999999655 57788999999999998874

>1wyh_A SLIM 2, skeletal muscle LIM-protein 2; structural genomics, riken structural genomics/proteomics initiative, RSGI, NPPSFA; NMR {Homo sapiens} SCOP: g.39.1.3 g.39.1.3

Probab=99.02  E-value=4.7e-12  Score=84.64  Aligned_cols=53  Identities=25%  Similarity=0.426  Sum_probs=45.5

Q ss_pred             CCChHHHHHHHHhHHHhhhhhhhhhhcceeccCCccccccceeeeccchhhhhh
Q psy17504          2 GISSSELVMRARDLVFHLHCFTCISCGILLTKGDLFGMRDEMIYCRPHYEILRH   55 (196)
Q Consensus         2 ~i~~~~~v~~a~~~~~H~~CF~C~~C~~~L~~G~~f~~~~~~~~C~~~y~~~~~   55 (196)
                      .|.+.+.+++|.++.||..||+|..|+++|. +..|...++++||+.||..++.
T Consensus        14 ~I~~~~~~~~a~~~~~H~~CF~C~~C~~~L~-~~~~~~~~~~~yC~~cy~~~f~   66 (72)
T 1wyh_A           14 TVMPGSRKLEYGGQTWHEHCFLCSGCEQPLG-SRSFVPDKGAHYCVPCYENKFA   66 (72)
T ss_dssp             BCCSSSCEECSTTCCEETTTCBCTTTCCBTT-TSCEEEETTEEEEHHHHHHHTS
T ss_pred             ccccCccEEEECccccCcccCeECCCCCcCC-CCccCCcCCeEECHHHHHHHcc
Confidence            3555567788999999999999999999994 5578888999999999998875

>1x4k_A Skeletal muscle LIM-protein 3; LIM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: g.39.1.3 g.39.1.3

Probab=99.01  E-value=5.1e-12  Score=84.48  Aligned_cols=53  Identities=25%  Similarity=0.456  Sum_probs=45.8

Q ss_pred             CCChHHHHHHHHhHHHhhhhhhhhhhcceeccCCccccccceeeeccchhhhhh
Q psy17504          2 GISSSELVMRARDLVFHLHCFTCISCGILLTKGDLFGMRDEMIYCRPHYEILRH   55 (196)
Q Consensus         2 ~i~~~~~v~~a~~~~~H~~CF~C~~C~~~L~~G~~f~~~~~~~~C~~~y~~~~~   55 (196)
                      .|.+.+.+++|.++.||..||+|..|+++|. +..|...++++||+.||..++.
T Consensus        14 ~I~~~~~~~~a~~~~~H~~CF~C~~C~~~L~-~~~~~~~~~~~yC~~cy~~~f~   66 (72)
T 1x4k_A           14 TIMPGTRKMEYKGSSWHETCFICHRCQQPIG-TKSFIPKDNQNFCVPCYEKQHA   66 (72)
T ss_dssp             CCCSSSCEEEETTEEEETTTTCCSSSCCCCC-SSSEEEETTEEEEHHHHHHHTS
T ss_pred             cccCCceEEEECcCeecccCCcccccCCccC-CCccCccCCeEECHHHHhHHhC
Confidence            4555567788999999999999999999995 4478889999999999998875

>1zq3_P PRD-4, homeotic bicoid protein; protein-DNA complex, double helix, helix-turn-helix; NMR {Drosophila melanogaster} SCOP: a.4.1.1

Probab=99.01  E-value=2e-10  Score=76.36  Aligned_cols=46  Identities=24%  Similarity=0.352  Sum_probs=44.2

Q ss_pred             cchhhcccchhhHhhhhhhhcccCCCChHHHHHHHHHhCcchhhhc
Q psy17504        150 TKRMRTSFKHHQLRTMKSYFNINQNPDAKDLKQLAQKTGLSKRVLQ  195 (196)
Q Consensus       150 ~rR~RT~ft~~Ql~~L~~~F~~~~~p~~~~r~~La~~lgL~~~~Vq  195 (196)
                      +||.||.||..|+..|+..|..++||+...++.||..+||++.+|+
T Consensus         2 ~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~   47 (68)
T 1zq3_P            2 PRRTRTTFTSSQIAELEQHFLQGRYLTAPRLADLSAKLALGTAQVK   47 (68)
T ss_dssp             CSCCSCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHTSCHHHHH
T ss_pred             cCCCCCCcCHHHHHHHHHHHhcCCCcCHHHHHHHHHHhCcCHHHhh
Confidence            4778999999999999999999999999999999999999999997

>1jgg_A Segmentation protein EVEN-skipped; homeodomain, protein-DNA complex, transcription/DNA complex; 2.00A {Drosophila melanogaster} SCOP: a.4.1.1

Probab=99.00  E-value=1.9e-10  Score=74.56  Aligned_cols=45  Identities=22%  Similarity=0.332  Sum_probs=42.9

Q ss_pred             chhhcccchhhHhhhhhhhcccCCCChHHHHHHHHHhCcchhhhc
Q psy17504        151 KRMRTSFKHHQLRTMKSYFNINQNPDAKDLKQLAQKTGLSKRVLQ  195 (196)
Q Consensus       151 rR~RT~ft~~Ql~~L~~~F~~~~~p~~~~r~~La~~lgL~~~~Vq  195 (196)
                      ||.||.||..|+..|+..|..++||+...+++||..+||++.+|+
T Consensus         2 rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~   46 (60)
T 1jgg_A            2 RRYRTAFTRDQLGRLEKEFYKENYVSRPRRCELAAQLNLPESTIK   46 (60)
T ss_dssp             -CCCCCCCHHHHHHHHHHHHHCSCCCHHHHHHHHHHHTSCHHHHH
T ss_pred             CCCCCCCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHHCcCHHHHH
Confidence            578999999999999999999999999999999999999999997

>1ahd_P Antennapedia protein mutant; DNA binding protein/DNA; HET: DNA; NMR {Drosophila melanogaster} SCOP: a.4.1.1 PDB: 2hoa_A 1hom_A 1ftz_A

Probab=98.99  E-value=1.9e-10  Score=76.49  Aligned_cols=46  Identities=20%  Similarity=0.319  Sum_probs=44.0

Q ss_pred             cchhhcccchhhHhhhhhhhcccCCCChHHHHHHHHHhCcchhhhc
Q psy17504        150 TKRMRTSFKHHQLRTMKSYFNINQNPDAKDLKQLAQKTGLSKRVLQ  195 (196)
Q Consensus       150 ~rR~RT~ft~~Ql~~L~~~F~~~~~p~~~~r~~La~~lgL~~~~Vq  195 (196)
                      +||.||.||..|+..|+..|..++||+...+++||..+||++.+||
T Consensus         2 ~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~   47 (68)
T 1ahd_P            2 RKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIK   47 (68)
T ss_dssp             CSCTTCCCCHHHHHHHHHHHHHCSSCCTTHHHHHHHHHTCCHHHHH
T ss_pred             CCCCCCCcCHHHHHHHHHHHccCCCCCHHHHHHHHHHHCcCHhhhh
Confidence            3678999999999999999999999999999999999999999997

>2r5y_A Homeotic protein sex combs reduced; homeodomain; HET: DNA; 2.60A {Drosophila melanogaster} PDB: 2r5z_A*

Probab=98.99  E-value=2.2e-10  Score=79.91  Aligned_cols=48  Identities=25%  Similarity=0.360  Sum_probs=42.3

Q ss_pred             cccchhhcccchhhHhhhhhhhcccCCCChHHHHHHHHHhCcchhhhc
Q psy17504        148 QRTKRMRTSFKHHQLRTMKSYFNINQNPDAKDLKQLAQKTGLSKRVLQ  195 (196)
Q Consensus       148 ~k~rR~RT~ft~~Ql~~L~~~F~~~~~p~~~~r~~La~~lgL~~~~Vq  195 (196)
                      .+.||.||.||..|+..|+..|..++||+...|++||..+||++.+||
T Consensus        26 ~~~rr~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~   73 (88)
T 2r5y_A           26 GETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIK   73 (88)
T ss_dssp             -----CCCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHTTCCHHHHH
T ss_pred             CCCCCCCCCcCHHHHHHHHHHHhccCCCCHHHHHHHHHHhCcCHHHhh
Confidence            356789999999999999999999999999999999999999999997

>1fjl_A Paired protein; DNA-binding protein, paired BOX, transcription regulation; HET: DNA; 2.00A {Drosophila melanogaster} SCOP: a.4.1.1 PDB: 3a01_B

Probab=98.99  E-value=1.9e-10  Score=78.97  Aligned_cols=49  Identities=33%  Similarity=0.512  Sum_probs=45.4

Q ss_pred             ccccchhhcccchhhHhhhhhhhcccCCCChHHHHHHHHHhCcchhhhc
Q psy17504        147 HQRTKRMRTSFKHHQLRTMKSYFNINQNPDAKDLKQLAQKTGLSKRVLQ  195 (196)
Q Consensus       147 ~~k~rR~RT~ft~~Ql~~L~~~F~~~~~p~~~~r~~La~~lgL~~~~Vq  195 (196)
                      .++.||.||.|+..|+..|+..|..++||+...+++||..+||++.+|+
T Consensus        15 ~~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~   63 (81)
T 1fjl_A           15 KRKQRRSRTTFSASQLDELERAFERTQYPDIYTREELAQRTNLTEARIQ   63 (81)
T ss_dssp             --CCCCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHH
T ss_pred             cCCCCCCCCCCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHHCcCHHHHH
Confidence            4567889999999999999999999999999999999999999999997

>3rkq_A Homeobox protein NKX-2.5; helix-turn-helix, DNA binding, nucleus, transcription-DNA CO; 1.70A {Homo sapiens}

Probab=98.98  E-value=2.9e-10  Score=72.84  Aligned_cols=46  Identities=20%  Similarity=0.274  Sum_probs=43.7

Q ss_pred             cchhhcccchhhHhhhhhhhcccCCCChHHHHHHHHHhCcchhhhc
Q psy17504        150 TKRMRTSFKHHQLRTMKSYFNINQNPDAKDLKQLAQKTGLSKRVLQ  195 (196)
Q Consensus       150 ~rR~RT~ft~~Ql~~L~~~F~~~~~p~~~~r~~La~~lgL~~~~Vq  195 (196)
                      +||.||.|+..|+..|+..|..++||+...+++||..+||++.+||
T Consensus         2 ~rr~Rt~~t~~q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~   47 (58)
T 3rkq_A            2 RRKPRVLFSQAQVYELERRFKQQRYLSAPERDQLASVLKLTSTQVK   47 (58)
T ss_dssp             CCCCCCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHTCCHHHHH
T ss_pred             cCCCCCCcCHHHHHHHHHHHHHcCCCCHHHHHHHHHHhCcCHHHHH
Confidence            3568999999999999999999999999999999999999999997

>1b8i_A Ultrabithorax, protein (ultrabithorax homeotic protein IV); DNA binding, homeodomain, homeotic proteins, development, specificity; HET: DNA; 2.40A {Drosophila melanogaster} SCOP: a.4.1.1 PDB: 9ant_A*

Probab=98.97  E-value=2.4e-10  Score=78.60  Aligned_cols=47  Identities=17%  Similarity=0.280  Sum_probs=41.4

Q ss_pred             ccchhhcccchhhHhhhhhhhcccCCCChHHHHHHHHHhCcchhhhc
Q psy17504        149 RTKRMRTSFKHHQLRTMKSYFNINQNPDAKDLKQLAQKTGLSKRVLQ  195 (196)
Q Consensus       149 k~rR~RT~ft~~Ql~~L~~~F~~~~~p~~~~r~~La~~lgL~~~~Vq  195 (196)
                      +.||.||.||..|+..|+..|..++||+...|++||..+||++.+||
T Consensus        19 ~~rr~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~   65 (81)
T 1b8i_A           19 LRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALSLTERQIK   65 (81)
T ss_dssp             -----CCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHH
T ss_pred             CCCCCCcccCHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCHHHHH
Confidence            56789999999999999999999999999999999999999999997

>2ehe_A Four and A half LIM domains 3; FHL-3, skeletal muscle LIM- protein 2, SLIM 2, FHL3, SLIM2, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=98.97  E-value=1.3e-11  Score=84.68  Aligned_cols=54  Identities=24%  Similarity=0.386  Sum_probs=46.8

Q ss_pred             CCChHHHHHHHHhHHHhhhhhhhhhhcceeccCCccccccceeeeccchhhhhhc
Q psy17504          2 GISSSELVMRARDLVFHLHCFTCISCGILLTKGDLFGMRDEMIYCRPHYEILRHR   56 (196)
Q Consensus         2 ~i~~~~~v~~a~~~~~H~~CF~C~~C~~~L~~G~~f~~~~~~~~C~~~y~~~~~~   56 (196)
                      .|.+.+.+++|.++.||..||+|..|+++| .+..|...++++||+.||..++..
T Consensus        24 ~I~~~~~~~~a~~~~~H~~CF~C~~C~~~L-~~~~f~~~~~~~~C~~c~~~~~~~   77 (82)
T 2ehe_A           24 LIGHDSRELFYEDRHFHEGCFRCCRCQRSL-ADEPFTCQDSELLCNDCYCSAFSS   77 (82)
T ss_dssp             BCCSSCCBCCCSSCCCBTTTSBCTTTCCBC-SSCCEEEETTEEEETTTSSCCGGG
T ss_pred             ccccCcEEEEeCCccccccCCeecCCCCcc-CCCccEeeCCEEECHHHHhhhcCC
Confidence            355567788899999999999999999999 477888899999999999888753

>1yz8_P Pituitary homeobox 2; DNA binding protein, transcription/DNA complex; NMR {Homo sapiens} SCOP: a.4.1.1 PDB: 2l7f_P 2lkx_A* 2l7m_P

Probab=98.97  E-value=1.6e-10  Score=76.80  Aligned_cols=47  Identities=28%  Similarity=0.461  Sum_probs=44.8

Q ss_pred             ccchhhcccchhhHhhhhhhhcccCCCChHHHHHHHHHhCcchhhhc
Q psy17504        149 RTKRMRTSFKHHQLRTMKSYFNINQNPDAKDLKQLAQKTGLSKRVLQ  195 (196)
Q Consensus       149 k~rR~RT~ft~~Ql~~L~~~F~~~~~p~~~~r~~La~~lgL~~~~Vq  195 (196)
                      +.||.||.||..|+..|+..|..++||+...+++||..+||++.+|+
T Consensus         2 ~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~   48 (68)
T 1yz8_P            2 SQRRQRTHFTSQQLQQLEATFQRNRYPDMSTREEIAVWTNLTEARVR   48 (68)
T ss_dssp             CSSCSCCCCCHHHHHHHHHHHTTCSSCCTTTTTHHHHHTTSCHHHHH
T ss_pred             CCCCCCCCCCHHHHHHHHHHHHccCCCCHHHHHHHHHHHCcCHHHHH
Confidence            45788999999999999999999999999999999999999999997

>3nar_A ZHX1, zinc fingers and homeoboxes protein 1; corepressor, homeodomain, structural genomics, oxford production facility, OPPF, transcription; 2.60A {Homo sapiens}

Probab=98.97  E-value=2.4e-10  Score=81.03  Aligned_cols=48  Identities=23%  Similarity=0.306  Sum_probs=42.9

Q ss_pred             cccchhhcccchhhHhhhhhhhcccCCCChHHHHHHHHHhCcchhhhc
Q psy17504        148 QRTKRMRTSFKHHQLRTMKSYFNINQNPDAKDLKQLAQKTGLSKRVLQ  195 (196)
Q Consensus       148 ~k~rR~RT~ft~~Ql~~L~~~F~~~~~p~~~~r~~La~~lgL~~~~Vq  195 (196)
                      ...+|.||.||..|+..|+..|..++||+...+++||..+||++++||
T Consensus        23 ~~~~r~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~L~~~qV~   70 (96)
T 3nar_A           23 SGSTGKICKKTPEQLHMLKSAFVRTQWPSPEEYDKLAKESGLARTDIV   70 (96)
T ss_dssp             ----CCSSSSCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHCCCHHHHH
T ss_pred             CCCCCCCccCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHhCCCHHHee
Confidence            455678999999999999999999999999999999999999999997

>1x4l_A Skeletal muscle LIM-protein 3; LIM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: g.39.1.3 g.39.1.3

Probab=98.96  E-value=7.1e-12  Score=83.88  Aligned_cols=49  Identities=20%  Similarity=0.394  Sum_probs=43.5

Q ss_pred             HHHHHHHHhHHHhhhhhhhhhhcceeccCCccccccceeeeccchhhhhh
Q psy17504          6 SELVMRARDLVFHLHCFTCISCGILLTKGDLFGMRDEMIYCRPHYEILRH   55 (196)
Q Consensus         6 ~~~v~~a~~~~~H~~CF~C~~C~~~L~~G~~f~~~~~~~~C~~~y~~~~~   55 (196)
                      .+.++.|.++.||..||+|..|+++| .+..|..+++++||+.||..++.
T Consensus        20 ~~~~~~a~~~~wH~~CF~C~~C~~~L-~~~~f~~~~g~~yC~~c~~~~~~   68 (72)
T 1x4l_A           20 GTKYISFEERQWHNDCFNCKKCSLSL-VGRGFLTERDDILCPDCGKDISG   68 (72)
T ss_dssp             SCSCEECSSCEECTTTCBCSSSCCBC-TTSCCEECSSSEECHHHHHTCCC
T ss_pred             CcceEEECCcccCcccCEeccCCCcC-CCCccEeECCEEEChhHcCcccC
Confidence            34677889999999999999999999 57788889999999999998774

>1ftt_A TTF-1 HD, thyroid transcription factor 1 homeodomain; DNA binding protein; NMR {Rattus norvegicus} SCOP: a.4.1.1

Probab=98.96  E-value=3.3e-10  Score=75.27  Aligned_cols=46  Identities=17%  Similarity=0.273  Sum_probs=44.1

Q ss_pred             cchhhcccchhhHhhhhhhhcccCCCChHHHHHHHHHhCcchhhhc
Q psy17504        150 TKRMRTSFKHHQLRTMKSYFNINQNPDAKDLKQLAQKTGLSKRVLQ  195 (196)
Q Consensus       150 ~rR~RT~ft~~Ql~~L~~~F~~~~~p~~~~r~~La~~lgL~~~~Vq  195 (196)
                      .||.||.||..|+..|+..|..++||+...+++||..+||++.+|+
T Consensus         2 ~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~   47 (68)
T 1ftt_A            2 RRKRRVLFSQAQVYELERRFKQQKYLSAPEREHLASMIHLTPTQVK   47 (68)
T ss_dssp             CSSSCSSCCHHHHHHHHHHHHHSSSCCHHHHHHHHHHHTSCHHHHH
T ss_pred             CCCCCCccCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCHHHhH
Confidence            4678999999999999999999999999999999999999999997

>1x63_A Skeletal muscle LIM-protein 1; LIM domain, four and A half LIM domains protein 1, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: g.39.1.3 g.39.1.3

Probab=98.95  E-value=1.1e-11  Score=84.90  Aligned_cols=54  Identities=24%  Similarity=0.449  Sum_probs=46.3

Q ss_pred             CCChHHHHHHHHhHHHhhhhhhhhhhcceeccCCccccccceeeeccchhhhhhc
Q psy17504          2 GISSSELVMRARDLVFHLHCFTCISCGILLTKGDLFGMRDEMIYCRPHYEILRHR   56 (196)
Q Consensus         2 ~i~~~~~v~~a~~~~~H~~CF~C~~C~~~L~~G~~f~~~~~~~~C~~~y~~~~~~   56 (196)
                      .|.+.+.+++|.++.||..||+|..|+++|.. ..|...++++||+.||..++..
T Consensus        24 ~I~~~~~~~~a~~~~~H~~CF~C~~C~~~L~~-~~~~~~~~~~yC~~cy~~~f~~   77 (82)
T 1x63_A           24 AIVAGDQNVEYKGTVWHKDCFTCSNCKQVIGT-GSFFPKGEDFYCVTCHETKFAS   77 (82)
T ss_dssp             BCCSSSCEEECSSCEEETTTCCCSSSCCCCTT-SCEEEETTEEEEHHHHHHHTSC
T ss_pred             ccccCceEEEECccccccccCchhhCCCccCC-CccEeeCCEEECHHHHHHHhCC
Confidence            35566777889999999999999999999954 4788889999999999998864

>2co8_A NEDD9 interacting protein with calponin homology and LIM domains; zinc finger protein, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: g.39.1.3 g.39.1.3

Probab=98.95  E-value=2.2e-11  Score=83.83  Aligned_cols=52  Identities=25%  Similarity=0.435  Sum_probs=41.9

Q ss_pred             CChHHHHHHHHhHHHhhhhhhhhhhcceeccCCccc-cccceeeeccchhhhhh
Q psy17504          3 ISSSELVMRARDLVFHLHCFTCISCGILLTKGDLFG-MRDEMIYCRPHYEILRH   55 (196)
Q Consensus         3 i~~~~~v~~a~~~~~H~~CF~C~~C~~~L~~G~~f~-~~~~~~~C~~~y~~~~~   55 (196)
                      |...++|+ +.+++||..||+|..|+++|..+..+. .+++++||+.||..++.
T Consensus        25 I~~~e~v~-a~~~~wH~~CF~C~~C~~~L~~~~~~~~~~~g~~yC~~~y~~~~~   77 (82)
T 2co8_A           25 LYVLERLC-VNGHFFHRSCFRCHTCEATLWPGGYEQHPGDGHFYCLQHLPQTDS   77 (82)
T ss_dssp             CCTTTBCC-BTTBCCBTTTCBCSSSCCBCCTTSEECCTTTCCCEETTTCCCCCC
T ss_pred             cccceEEE-ECCCeeCCCcCEEcCCCCCcCCCceeEeCcCCEEEChHHHHhhhc
Confidence            44455554 889999999999999999996555443 47999999999998775

>2k40_A Homeobox expressed in ES cells 1; thermostable homeodomain variant, DNA binding protein, developmental protein, disease mutation, DNA-binding; NMR {Homo sapiens}

Probab=98.95  E-value=4.5e-10  Score=74.34  Aligned_cols=45  Identities=33%  Similarity=0.514  Sum_probs=43.6

Q ss_pred             chhhcccchhhHhhhhhhhcccCCCChHHHHHHHHHhCcchhhhc
Q psy17504        151 KRMRTSFKHHQLRTMKSYFNINQNPDAKDLKQLAQKTGLSKRVLQ  195 (196)
Q Consensus       151 rR~RT~ft~~Ql~~L~~~F~~~~~p~~~~r~~La~~lgL~~~~Vq  195 (196)
                      ||.||.||..|+..|+..|..++||+...++.||..+||++.+|+
T Consensus         2 rr~Rt~ft~~q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~   46 (67)
T 2k40_A            2 RRPRTAFTQNQIEVLENVFRVNCYPGIDILEDLAQKLNLELDRIQ   46 (67)
T ss_dssp             CCCSCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHTCCHHHHH
T ss_pred             cCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHHCcCHHHhh
Confidence            678999999999999999999999999999999999999999997

>1nyp_A Pinch protein; LIM domain, protein recognition, cell adhesion; NMR {Homo sapiens} SCOP: g.39.1.3 g.39.1.3 PDB: 1u5s_B

Probab=98.95  E-value=2.3e-11  Score=79.98  Aligned_cols=46  Identities=28%  Similarity=0.538  Sum_probs=41.2

Q ss_pred             HHHHHhHHHhhhhhhhhhhcceeccCCccccccceeeeccchhhhhh
Q psy17504          9 VMRARDLVFHLHCFTCISCGILLTKGDLFGMRDEMIYCRPHYEILRH   55 (196)
Q Consensus         9 v~~a~~~~~H~~CF~C~~C~~~L~~G~~f~~~~~~~~C~~~y~~~~~   55 (196)
                      ++.|.++.||..||+|..|+++| .+..|...++.+||+.||..+++
T Consensus        19 ~~~a~~~~~H~~CF~C~~C~~~L-~~~~~~~~~g~~yC~~~y~~~f~   64 (66)
T 1nyp_A           19 VVNAMGKQWHVEHFVCAKCEKPF-LGHRHYERKGLAYCETHYNQLFG   64 (66)
T ss_dssp             EECCTTSBEETTTCBCTTTCCBC-SSSCCEEETTEEECHHHHHHHCS
T ss_pred             EEEECccccccCcCEECCCCCCC-CCCceEeECCcEECHHHHHHHhC
Confidence            46788999999999999999999 56788889999999999998875

>1x68_A FHL5 protein; four-and-A-half LIM protein 5, zinc finger domain, AN actin- interacting protein, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: g.39.1.3 g.39.1.3

Probab=98.94  E-value=1.9e-11  Score=82.70  Aligned_cols=48  Identities=23%  Similarity=0.483  Sum_probs=42.7

Q ss_pred             HHHHHHHhHHHhhhhhhhhhhcceeccCCccccccceeeeccchhhhhh
Q psy17504          7 ELVMRARDLVFHLHCFTCISCGILLTKGDLFGMRDEMIYCRPHYEILRH   55 (196)
Q Consensus         7 ~~v~~a~~~~~H~~CF~C~~C~~~L~~G~~f~~~~~~~~C~~~y~~~~~   55 (196)
                      +.++.|.++.||..||+|..|+++| .+..|+..++++||+.||..++.
T Consensus        21 ~~~~~a~~~~wH~~CF~C~~C~~~L-~~~~f~~~~g~~yC~~cy~~~f~   68 (76)
T 1x68_A           21 AKFICFQDSQWHSECFNCGKCSVSL-VGKGFLTQNKEIFCQKCGSGMDT   68 (76)
T ss_dssp             CCEEEETTEEEEGGGCBCTTTCCBC-SSSCEEEETTEEEETTTTCCCCC
T ss_pred             ceeEEECCcccCcccCChhhCCCcC-CCCceEeECCEEECHHHhhhhhC
Confidence            3567889999999999999999999 47788889999999999988775

>1x2n_A Homeobox protein pknox1; homeobox domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: a.4.1.1

Probab=98.93  E-value=4.3e-10  Score=75.66  Aligned_cols=49  Identities=24%  Similarity=0.344  Sum_probs=45.2

Q ss_pred             cccchhhcccchhhHhhhhhhhcc---cCCCChHHHHHHHHHhCcchhhhcC
Q psy17504        148 QRTKRMRTSFKHHQLRTMKSYFNI---NQNPDAKDLKQLAQKTGLSKRVLQN  196 (196)
Q Consensus       148 ~k~rR~RT~ft~~Ql~~L~~~F~~---~~~p~~~~r~~La~~lgL~~~~Vq~  196 (196)
                      .+.+|.||.|+..|+..|+..|..   ++||+..++++||..+||++.+|++
T Consensus         5 ~~~rr~R~~~~~~q~~~Le~~f~~~~~~~yp~~~~r~~La~~~~L~~~qV~~   56 (73)
T 1x2n_A            5 SSGKNKRGVLPKHATNVMRSWLFQHIGHPYPTEDEKKQIAAQTNLTLLQVNN   56 (73)
T ss_dssp             SSSCCSSCCCCHHHHHHHHHHHHHTTTSCCCCHHHHHHHHHHHTCCHHHHHH
T ss_pred             CCCCCCCCcCCHHHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHCcCHHHHHH
Confidence            456778999999999999999976   9999999999999999999999973

>3a01_A Homeodomain-containing protein; homeodomain, protein-DNA complex, DNA-binding, homeobox, NUC developmental protein; 2.70A {Drosophila melanogaster}

Probab=98.93  E-value=4.4e-10  Score=79.29  Aligned_cols=48  Identities=19%  Similarity=0.294  Sum_probs=45.6

Q ss_pred             cccchhhcccchhhHhhhhhhhcccCCCChHHHHHHHHHhCcchhhhc
Q psy17504        148 QRTKRMRTSFKHHQLRTMKSYFNINQNPDAKDLKQLAQKTGLSKRVLQ  195 (196)
Q Consensus       148 ~k~rR~RT~ft~~Ql~~L~~~F~~~~~p~~~~r~~La~~lgL~~~~Vq  195 (196)
                      .+.||.||.||..|+..|+..|..++||+...|++||..+||++.+||
T Consensus        15 ~~~rr~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~L~~~qV~   62 (93)
T 3a01_A           15 PKRKKPRTSFTRIQVAELEKRFHKQKYLASAERAALARGLKMTDAQVK   62 (93)
T ss_dssp             CCCCCCCCCCCHHHHHHHHHHHHHCSCCCHHHHHHHHHTTTCCHHHHH
T ss_pred             CCCCCCCcCCCHHHHHHHHHHHHcCCCcCHHHHHHHHHHhCCChhhcc
Confidence            456789999999999999999999999999999999999999999997

>2dn0_A Zinc fingers and homeoboxes protein 3; triple homeobox 1 protein, KIAA0395, TIX1, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=98.92  E-value=5.6e-10  Score=75.74  Aligned_cols=46  Identities=30%  Similarity=0.456  Sum_probs=43.3

Q ss_pred             cchhhcccchhhHhhhhhhhcccCCCChHHHHHHHHHhCcchhhhc
Q psy17504        150 TKRMRTSFKHHQLRTMKSYFNINQNPDAKDLKQLAQKTGLSKRVLQ  195 (196)
Q Consensus       150 ~rR~RT~ft~~Ql~~L~~~F~~~~~p~~~~r~~La~~lgL~~~~Vq  195 (196)
                      +.+.||.||..|+..|+..|..++||+...+++||..+||++.+||
T Consensus         8 ~~~~R~~ft~~Ql~~Le~~F~~~~yp~~~~r~~La~~~~l~~~qV~   53 (76)
T 2dn0_A            8 ASIYKNKKSHEQLSALKGSFCRNQFPGQSEVEHLTKVTGLSTREVR   53 (76)
T ss_dssp             CCCCCCCCCHHHHHHHHHHHHHSSSCCSHHHHHHHHHHCCCHHHHH
T ss_pred             CCCCCccCCHHHHHHHHHHHhcCCCcCHHHHHHHHHHhCCChHHhh
Confidence            3446899999999999999999999999999999999999999997

>2ecc_A Homeobox and leucine zipper protein homez; homeobox domain, transcription factor, leucine zipper- containing factor, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: a.4.1.1

Probab=98.91  E-value=5.6e-10  Score=75.79  Aligned_cols=44  Identities=27%  Similarity=0.315  Sum_probs=41.0

Q ss_pred             hhcccchhhHhhhhhhhcccCCCChHHHHHHHHHhCcchhhhcC
Q psy17504        153 MRTSFKHHQLRTMKSYFNINQNPDAKDLKQLAQKTGLSKRVLQN  196 (196)
Q Consensus       153 ~RT~ft~~Ql~~L~~~F~~~~~p~~~~r~~La~~lgL~~~~Vq~  196 (196)
                      .|+.||.+||.+|+..|..++||+..+|++||..|||++.+||.
T Consensus         6 ~r~kfT~~Ql~~Le~~F~~~~YPs~~er~~LA~~tgLte~qIkv   49 (76)
T 2ecc_A            6 SGKRKTKEQLAILKSFFLQCQWARREDYQKLEQITGLPRPEIIQ   49 (76)
T ss_dssp             CCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTCCCHHHHHH
T ss_pred             CCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHHCcCHHHhhH
Confidence            45669999999999999999999999999999999999999973

>1wig_A KIAA1808 protein; LIM domain, zinc finger, metal-binding protein, structural genomics, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: g.39.1.3 g.39.1.3

Probab=98.90  E-value=4.3e-11  Score=80.53  Aligned_cols=48  Identities=21%  Similarity=0.505  Sum_probs=43.3

Q ss_pred             HHHHHHhHHHhhhhhhhhhhcceeccCCccccccceeeeccchhhhhh
Q psy17504          8 LVMRARDLVFHLHCFTCISCGILLTKGDLFGMRDEMIYCRPHYEILRH   55 (196)
Q Consensus         8 ~v~~a~~~~~H~~CF~C~~C~~~L~~G~~f~~~~~~~~C~~~y~~~~~   55 (196)
                      .++.|.++.||..||+|..|+++|..|..|++.++++||..||..++.
T Consensus        18 ~~v~a~~~~wH~~CF~C~~C~~~L~~~~~f~~~~~~~yC~~C~~~~~~   65 (73)
T 1wig_A           18 RVLEAGEKHYHPSCALCVRCGQMFAEGEEMYLQGSSIWHPACRQAART   65 (73)
T ss_dssp             CCBCCSSCCBCTTTSCCSSSCCCCCSSCCCEEETTEEECTTHHHHTSS
T ss_pred             eeEEeCCCCCCCCcCEeCCCCCCCCCCCeeEeeCCEEEChHHChHhhc
Confidence            456789999999999999999999668999999999999999988764

>1x6a_A LIMK-2, LIM domain kinase 2; LIM-kinase 2, zinc finger domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: g.39.1.3 g.39.1.3

Probab=98.90  E-value=4.2e-11  Score=81.89  Aligned_cols=50  Identities=24%  Similarity=0.676  Sum_probs=44.1

Q ss_pred             HHHHHHHhHHHhhhhhhhhhhcceeccCCcccc-ccceeeeccchhhhhhc
Q psy17504          7 ELVMRARDLVFHLHCFTCISCGILLTKGDLFGM-RDEMIYCRPHYEILRHR   56 (196)
Q Consensus         7 ~~v~~a~~~~~H~~CF~C~~C~~~L~~G~~f~~-~~~~~~C~~~y~~~~~~   56 (196)
                      +.+++|.++.||..||+|..|+++|..|..|.+ .++++||+.||..++..
T Consensus        27 ~~~~~a~~~~~H~~CF~C~~C~~~L~~g~~f~~~~~~~~~C~~c~~~~~~~   77 (81)
T 1x6a_A           27 GPFMVAGEFKYHPECFACMSCKVIIEDGDAYALVQHATLYCGKCHNEVVSG   77 (81)
T ss_dssp             SCCBCCTTCCBCTTSCBCTTTCCBCCTTSCEEECSSSCEEEHHHHHHHHCT
T ss_pred             ceEEEECCceeccccCCccCCCCccCCCCcEEEeeCCEEECHHHHHHHhcC
Confidence            456788999999999999999999977888884 89999999999988853

>1x62_A C-terminal LIM domain protein 1; PDZ and LIM domain protein 1, LIM domain protein CLP-36, contractIle protein, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: g.39.1.3 g.39.1.3

Probab=98.90  E-value=2.1e-11  Score=83.18  Aligned_cols=47  Identities=28%  Similarity=0.511  Sum_probs=42.0

Q ss_pred             HHHHHhHHHhhhhhhhhhhcceeccCCccccccceeeeccchhhhhhc
Q psy17504          9 VMRARDLVFHLHCFTCISCGILLTKGDLFGMRDEMIYCRPHYEILRHR   56 (196)
Q Consensus         9 v~~a~~~~~H~~CF~C~~C~~~L~~G~~f~~~~~~~~C~~~y~~~~~~   56 (196)
                      +++|.++.||..||+|..|+++| .+..|+..++++||+.||..++.+
T Consensus        29 ~~~a~~~~~H~~CF~C~~C~~~L-~~~~~~~~~g~~yC~~cy~~~~~p   75 (79)
T 1x62_A           29 FVKLRDRHRHPECYVCTDCGTNL-KQKGHFFVEDQIYCEKHARERVSG   75 (79)
T ss_dssp             CEECSSCEECTTTTSCSSSCCCH-HHHCCEESSSCEECHHHHHHHHSS
T ss_pred             EEEECcceeCcCcCeeCCCCCCC-CCCCeEeECCEEECHHHHHHHhCC
Confidence            67889999999999999999999 456788889999999999998864

>1b72_A Protein (homeobox protein HOX-B1); homeodomain, DNA, complex, DNA-binding protein, protein/DNA complex; HET: DNA; 2.35A {Homo sapiens} SCOP: a.4.1.1

Probab=98.90  E-value=7.9e-10  Score=78.46  Aligned_cols=47  Identities=19%  Similarity=0.311  Sum_probs=42.3

Q ss_pred             ccchhhcccchhhHhhhhhhhcccCCCChHHHHHHHHHhCcchhhhc
Q psy17504        149 RTKRMRTSFKHHQLRTMKSYFNINQNPDAKDLKQLAQKTGLSKRVLQ  195 (196)
Q Consensus       149 k~rR~RT~ft~~Ql~~L~~~F~~~~~p~~~~r~~La~~lgL~~~~Vq  195 (196)
                      +.+|.||.||..|+..|+..|..++||+...|++||..+||++.+||
T Consensus        33 ~~rr~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~   79 (97)
T 1b72_A           33 SPSGLRTNFTTRQLTELEKEFHFNKYLSRARRVEIAATLELNETQVK   79 (97)
T ss_dssp             ----CCCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHTCCHHHHH
T ss_pred             CCCCCCcCcCHHHHHHHHHHHhccCCCCHHHHHHHHHHhCCCHHHhH
Confidence            56778999999999999999999999999999999999999999997

>1x64_A Alpha-actinin-2 associated LIM protein; LIM domain, PDZ and LIM domain 3, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: g.39.1.3 g.39.1.3

Probab=98.88  E-value=4.8e-11  Score=83.21  Aligned_cols=48  Identities=27%  Similarity=0.545  Sum_probs=41.5

Q ss_pred             HHHHHHhHHHhhhhhhhhhhcceeccCCccccccceeeeccchhhhhhc
Q psy17504          8 LVMRARDLVFHLHCFTCISCGILLTKGDLFGMRDEMIYCRPHYEILRHR   56 (196)
Q Consensus         8 ~v~~a~~~~~H~~CF~C~~C~~~L~~G~~f~~~~~~~~C~~~y~~~~~~   56 (196)
                      .+++|.++.||..||+|..|++.|. +..|+..++++||+.||..++..
T Consensus        38 ~~~~a~~~~~H~~CF~C~~C~~~L~-~~~~~~~~g~~yC~~~y~~~f~p   85 (89)
T 1x64_A           38 AVVKARDKYRHPECFVCADCNLNLK-QKGYFFVEGELYCETHARARTSG   85 (89)
T ss_dssp             CCEESSSCEECTTTCCCSSSCCCTT-TSCCEEETTEEECHHHHHHHSSS
T ss_pred             cEEEECCceECccCCEecCCCCCCC-CCCeEeECCEEECHHHHHHHhCC
Confidence            4577899999999999999999995 44677789999999999988864

>2ly9_A Zinc fingers and homeoboxes protein 1; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative; NMR {Homo sapiens}

Probab=98.88  E-value=1e-09  Score=73.95  Aligned_cols=47  Identities=26%  Similarity=0.354  Sum_probs=44.6

Q ss_pred             ccchhhcccchhhHhhhhhhhcccCCCChHHHHHHHHHhCcchhhhc
Q psy17504        149 RTKRMRTSFKHHQLRTMKSYFNINQNPDAKDLKQLAQKTGLSKRVLQ  195 (196)
Q Consensus       149 k~rR~RT~ft~~Ql~~L~~~F~~~~~p~~~~r~~La~~lgL~~~~Vq  195 (196)
                      ..++.||.||..|+..|+..|..++||+...+++||..+||++.+||
T Consensus         5 ~~~~~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~   51 (74)
T 2ly9_A            5 DSFGIRAKKTKEQLAELKVSYLKNQFPHDSEIIRLMKITGLTKGEIK   51 (74)
T ss_dssp             CCCCTTCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHCCCHHHHH
T ss_pred             CCCCCCcCCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHhCcCHHHee
Confidence            45678999999999999999999999999999999999999999997

>2d8x_A Protein pinch; LIM domain, pinch protein, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: g.39.1.3 g.39.1.3

Probab=98.88  E-value=6.3e-11  Score=78.75  Aligned_cols=48  Identities=25%  Similarity=0.404  Sum_probs=42.0

Q ss_pred             HHHHHHhHHHhhhhhhhhhhcceeccCCccccccceeeeccchhhhhhc
Q psy17504          8 LVMRARDLVFHLHCFTCISCGILLTKGDLFGMRDEMIYCRPHYEILRHR   56 (196)
Q Consensus         8 ~v~~a~~~~~H~~CF~C~~C~~~L~~G~~f~~~~~~~~C~~~y~~~~~~   56 (196)
                      .+++|.++.||..||+|..|+++|..+ .|...++++||+.||..++..
T Consensus        18 ~~~~a~~~~~H~~CF~C~~C~~~L~~~-~f~~~~g~~yC~~c~~~~~~~   65 (70)
T 2d8x_A           18 RVIKAMNNSWHPECFRCDLCQEVLADI-GFVKNAGRHLCRPCHNREKAS   65 (70)
T ss_dssp             CCEEETTEEECTTTSBCSSSCCBCSSS-CCEEETTEEECHHHHHHHHCC
T ss_pred             eEEEECcccccccCCEeCCCCCcCCCC-ccEeECCeEECHHHhhhhcCC
Confidence            356789999999999999999999544 688889999999999998864

>2cur_A Skeletal muscle LIM-protein 1; four and A half LIM domains protein 1, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: g.39.1.3 g.39.1.3

Probab=98.87  E-value=9.3e-11  Score=77.70  Aligned_cols=46  Identities=26%  Similarity=0.637  Sum_probs=41.8

Q ss_pred             HHHHHhHHHhhhhhhhhhhcceeccCCccccccceeeeccchhhhhh
Q psy17504          9 VMRARDLVFHLHCFTCISCGILLTKGDLFGMRDEMIYCRPHYEILRH   55 (196)
Q Consensus         9 v~~a~~~~~H~~CF~C~~C~~~L~~G~~f~~~~~~~~C~~~y~~~~~   55 (196)
                      ++.+.++.||..||+|..|+++| .+..|.+.++++||+.||..++.
T Consensus        19 ~~~a~~~~~H~~CF~C~~C~~~L-~~~~~~~~~~~~yC~~cy~~~f~   64 (69)
T 2cur_A           19 GITYQDQPWHADCFVCVTCSKKL-AGQRFTAVEDQYYCVDCYKNFVS   64 (69)
T ss_dssp             CEEETTEEECTTTTBCTTTCCBC-TTSCEEECSSCEEEHHHHHHHHT
T ss_pred             eEEECccccccCcCEECCCCCCC-CCCccEeECCEEECHHHhHHHhc
Confidence            46788999999999999999999 47789889999999999998875

>2cuf_A FLJ21616 protein; homeobox domain, hepatocyte transcription factor, structural genomics, loop insertion, NPPSFA; NMR {Homo sapiens} SCOP: a.4.1.1

Probab=98.87  E-value=8.9e-10  Score=77.90  Aligned_cols=49  Identities=24%  Similarity=0.388  Sum_probs=46.2

Q ss_pred             ccccchhhcccchhhHhhhhhhhcccCCCChHHHHHHHHHhC---------------cchhhhc
Q psy17504        147 HQRTKRMRTSFKHHQLRTMKSYFNINQNPDAKDLKQLAQKTG---------------LSKRVLQ  195 (196)
Q Consensus       147 ~~k~rR~RT~ft~~Ql~~L~~~F~~~~~p~~~~r~~La~~lg---------------L~~~~Vq  195 (196)
                      ..+.||.||.|+..|+..|+..|+.++||+...|++||..++               |++.+|+
T Consensus         4 ~~~~rr~R~~ft~~ql~~Le~~F~~~~yP~~~~r~~lA~~l~~~~~~~~~~~~~~~~ls~~qV~   67 (95)
T 2cuf_A            4 GSSGRGSRFTWRKECLAVMESYFNENQYPDEAKREEIANACNAVIQKPGKKLSDLERVTSLKVY   67 (95)
T ss_dssp             SSCCCCCSCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHHHHHCCTTCCCCTTTCCCHHHHH
T ss_pred             CCCCCCCCCcCCHHHHHHHHHHHhcCCCCCHHHHHHHHHHHCchhhcccccccccCcCCHHHHH
Confidence            446788999999999999999999999999999999999999               9999987

>2xjy_A Rhombotin-2; oncoprotein, T-cell leukemia, proto-oncogene, transcription, developmental protein; 2.40A {Homo sapiens} PDB: 2xjz_A

Probab=98.86  E-value=5.1e-11  Score=88.54  Aligned_cols=53  Identities=30%  Similarity=0.614  Sum_probs=47.8

Q ss_pred             CChHHHHHHHHhHHHhhhhhhhhhhcceeccCCccccccceeeeccchhhhhh
Q psy17504          3 ISSSELVMRARDLVFHLHCFTCISCGILLTKGDLFGMRDEMIYCRPHYEILRH   55 (196)
Q Consensus         3 i~~~~~v~~a~~~~~H~~CF~C~~C~~~L~~G~~f~~~~~~~~C~~~y~~~~~   55 (196)
                      |.+.|.+|+|.+..||..||+|..|+++|..|+.|.+.++++||..||..+++
T Consensus        76 I~~~e~~~~a~~~~~H~~CF~C~~C~~~L~~g~~f~~~~~~~~C~~c~~~~~~  128 (131)
T 2xjy_A           76 IRAYEMTMRVKDKVYHLECFKCAACQKHFCVGDRYLLINSDIVCEQDIYEWTK  128 (131)
T ss_dssp             ECTTSEEEEETTEEEEGGGCBCTTTCCBCCTTCEEEEETTEEEEGGGHHHHHH
T ss_pred             cCccceeEeeCCceECccCcccCCCCCCCCCCCEEEEECCEEEcHHHHHHHhh
Confidence            55566788899999999999999999999779999999999999999998875

>2cu8_A Cysteine-rich protein 2; CRP2, CRIP2, ESP1 protein, zinc-binding, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: g.39.1.3 g.39.1.3

Probab=98.85  E-value=6.2e-11  Score=80.12  Aligned_cols=52  Identities=25%  Similarity=0.422  Sum_probs=43.2

Q ss_pred             CChHHHHHHHHhHHHhhhhhhhhhhcceeccCCccccccceeeec-cchhhhhhc
Q psy17504          3 ISSSELVMRARDLVFHLHCFTCISCGILLTKGDLFGMRDEMIYCR-PHYEILRHR   56 (196)
Q Consensus         3 i~~~~~v~~a~~~~~H~~CF~C~~C~~~L~~G~~f~~~~~~~~C~-~~y~~~~~~   56 (196)
                      |.+.++| .|.++.||..||+|..|+++|. +..|..+++++||+ .||..++..
T Consensus        19 I~~~~~v-~a~~~~~H~~CF~C~~C~~~L~-~~~~~~~~g~~yC~~~cy~~~f~~   71 (76)
T 2cu8_A           19 VYFAEKV-SSLGKDWHKFCLKCERCSKTLT-PGGHAEHDGKPFCHKPCYATLFGS   71 (76)
T ss_dssp             CCTTTEE-EETTEEEETTTCBCSSSCCBCC-TTSCEEETTEEECTTTHHHHHSCS
T ss_pred             eECCeEE-EECCeEeeCCCCCCCCCCCccC-CCceEeECCEEecchHHHHHhccc
Confidence            4444543 5889999999999999999994 66788899999999 799988753

>3a02_A Homeobox protein aristaless; homeodomain, developmental protein, DNA-binding, N gene regulation; 1.00A {Drosophila melanogaster} PDB: 3lnq_A 3cmy_A

Probab=98.85  E-value=1.4e-09  Score=70.39  Aligned_cols=43  Identities=28%  Similarity=0.432  Sum_probs=39.4

Q ss_pred             hhcccchhhHhhhhhhhcccCCCChHHHHHHHHHhCcchhhhc
Q psy17504        153 MRTSFKHHQLRTMKSYFNINQNPDAKDLKQLAQKTGLSKRVLQ  195 (196)
Q Consensus       153 ~RT~ft~~Ql~~L~~~F~~~~~p~~~~r~~La~~lgL~~~~Vq  195 (196)
                      .||.||..|+..|+..|..++||+...+++||..+||++.+|+
T Consensus         2 ~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~   44 (60)
T 3a02_A            2 SHMTFTSFQLEELEKAFSRTHYPDVFTREELAMKIGLTEARIQ   44 (60)
T ss_dssp             ---CCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTSCHHHHH
T ss_pred             CCcccCHHHHHHHHHHHHcCCCcCHHHHHHHHHHHCcCHHHHH
Confidence            5899999999999999999999999999999999999999997

>2d8z_A Four and A half LIM domains 2; skeletal muscle LIM-protein 3, LIM-domain protein DRAL, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: g.39.1.3 g.39.1.3

Probab=98.85  E-value=8.3e-11  Score=78.10  Aligned_cols=45  Identities=31%  Similarity=0.671  Sum_probs=40.9

Q ss_pred             HHHHhHHHhhhhhhhhhhcceeccCCccccccceeeeccchhhhhh
Q psy17504         10 MRARDLVFHLHCFTCISCGILLTKGDLFGMRDEMIYCRPHYEILRH   55 (196)
Q Consensus        10 ~~a~~~~~H~~CF~C~~C~~~L~~G~~f~~~~~~~~C~~~y~~~~~   55 (196)
                      +.|.++.||..||+|..|+++| .+..|...++++||+.||..++.
T Consensus        20 ~~a~~~~~H~~CF~C~~C~~~L-~~~~~~~~~~~~yC~~cy~~~f~   64 (70)
T 2d8z_A           20 VTYREQPWHKECFVCTACRKQL-SGQRFTARDDFAYCLNCFCDLYA   64 (70)
T ss_dssp             EESSSSEEETTTSBCSSSCCBC-TTSCCEESSSSEECHHHHHHHTC
T ss_pred             EEECccccCCCCCccCCCCCcC-CcCceEeeCCeEECHHHHHHHhc
Confidence            5788999999999999999999 57788889999999999998875

>2hi3_A Homeodomain-only protein; transcription; NMR {Mus musculus} SCOP: a.4.1.1

Probab=98.84  E-value=1.4e-09  Score=73.14  Aligned_cols=45  Identities=24%  Similarity=0.375  Sum_probs=42.7

Q ss_pred             chhhcccchhhHhhhhhhhcc-cCCCChHHHHHHHHHhCcchhhhc
Q psy17504        151 KRMRTSFKHHQLRTMKSYFNI-NQNPDAKDLKQLAQKTGLSKRVLQ  195 (196)
Q Consensus       151 rR~RT~ft~~Ql~~L~~~F~~-~~~p~~~~r~~La~~lgL~~~~Vq  195 (196)
                      ++.||.||..|+..|+..|.. ++||+...+++||..+||++.+||
T Consensus         3 ~k~Rt~ft~~Q~~~Le~~F~~~~~yp~~~~r~~LA~~~~l~~~qV~   48 (73)
T 2hi3_A            3 AQTVSGPTEDQVEILEYNFNKVNKHPDPTTLCLIAAEAGLTEEQTQ   48 (73)
T ss_dssp             CSCCSSCCHHHHHHHHHHHHHTTSSCCHHHHHHHHHHHTSCHHHHH
T ss_pred             CCCCCCCCHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHCcCHHHHH
Confidence            467899999999999999995 999999999999999999999997

>2egq_A FHL1 protein; LIM domain, four and A half LIM domains protein 1, skeletal muscle LIM- protein 1, SLIM 1, structural genomics NPPSFA; NMR {Homo sapiens}

Probab=98.84  E-value=3.9e-11  Score=81.17  Aligned_cols=46  Identities=26%  Similarity=0.533  Sum_probs=40.5

Q ss_pred             HHHHHHHhHHHhhhhhhhhhhcceeccCCccccccceeeeccchhhh
Q psy17504          7 ELVMRARDLVFHLHCFTCISCGILLTKGDLFGMRDEMIYCRPHYEIL   53 (196)
Q Consensus         7 ~~v~~a~~~~~H~~CF~C~~C~~~L~~G~~f~~~~~~~~C~~~y~~~   53 (196)
                      +.++.|.++.||..||+|..|+++| .+..|...++++||+.||..|
T Consensus        32 ~~~~~a~~~~~H~~CF~C~~C~~~L-~~~~f~~~~~~~yC~~cy~~l   77 (77)
T 2egq_A           32 SSVVAYEGQSWHDYCFHCKKCSVNL-ANKRFVFHQEQVYCPDCAKKL   77 (77)
T ss_dssp             CCEEEETTEEEETTTCBCSSSCCBC-TTSCCCEETTEECCHHHHHHC
T ss_pred             ceeEEECcceeCcccCEehhcCCCC-CCCccEeECCEEEChHHhccC
Confidence            3567789999999999999999999 477888899999999999753

>1du6_A PBX1, homeobox protein PBX1; homeodomain, gene regulation; NMR {Mus musculus} SCOP: a.4.1.1

Probab=98.84  E-value=1.5e-09  Score=71.08  Aligned_cols=47  Identities=19%  Similarity=0.327  Sum_probs=44.2

Q ss_pred             cchhhcccchhhHhhhhhhh---cccCCCChHHHHHHHHHhCcchhhhcC
Q psy17504        150 TKRMRTSFKHHQLRTMKSYF---NINQNPDAKDLKQLAQKTGLSKRVLQN  196 (196)
Q Consensus       150 ~rR~RT~ft~~Ql~~L~~~F---~~~~~p~~~~r~~La~~lgL~~~~Vq~  196 (196)
                      .++.||.|+..|+..|+..|   ..++||+..++++||..+||++.+|++
T Consensus         3 ~rr~R~~ft~~q~~~Le~~f~~~~~~~yp~~~~r~~La~~~~L~~~qV~~   52 (64)
T 1du6_A            3 GHIEGRHMNKQATEILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSN   52 (64)
T ss_dssp             CCCCCCSSTTTHHHHHHHHHHHTTTSCCCCHHHHHHHHHHHTSCHHHHHH
T ss_pred             CCCCCCcCCHHHHHHHHHHHHHcccCCCCCHHHHHHHHHHHCcCHHHHHH
Confidence            46789999999999999999   999999999999999999999999973

>2l4z_A DNA endonuclease RBBP8, LIM domain transcription LMO4; protein-protein interaction, LIM-interaction DOM LMO4, RBBP8/CTIP, LIM-only protein; HET: DNA; NMR {Homo sapiens}

Probab=98.84  E-value=8.5e-11  Score=87.06  Aligned_cols=46  Identities=33%  Similarity=0.540  Sum_probs=41.4

Q ss_pred             HHHHHhHHHhhhhhhhhhhcceec-cCCccccccceeeeccchhhhh
Q psy17504          9 VMRARDLVFHLHCFTCISCGILLT-KGDLFGMRDEMIYCRPHYEILR   54 (196)
Q Consensus         9 v~~a~~~~~H~~CF~C~~C~~~L~-~G~~f~~~~~~~~C~~~y~~~~   54 (196)
                      ++.|.++.||..||+|..|++.|. .|..|+.+++++||+.||..+|
T Consensus        76 ~v~a~~~~wH~~CF~C~~C~~~L~~~g~~f~~~dg~~yC~~cy~~~F  122 (123)
T 2l4z_A           76 LLYAMDSYWHSRCLKCSSCQAQLGDIGTSSYTKSGMILCRNDYIRLF  122 (123)
T ss_dssp             EEEETTEEEETTTSBCTTTCCBGGGTTCCCBCSSSCCBCHHHHHHHC
T ss_pred             EEEeCCcEEcccccCcCcCCCcccccCCceEEECCEEeCHHHhhhhc
Confidence            467889999999999999999996 3778999999999999999876

>2da6_A Hepatocyte nuclear factor 1-beta; homeobox domain, three helices with the DNA binding helix- turn-helix motif, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=98.84  E-value=1.4e-09  Score=77.70  Aligned_cols=48  Identities=10%  Similarity=0.190  Sum_probs=44.7

Q ss_pred             cccchhhcccchhhHhhhhhhhcccCCCChHHHHHHHHHh---------------------Ccchhhhc
Q psy17504        148 QRTKRMRTSFKHHQLRTMKSYFNINQNPDAKDLKQLAQKT---------------------GLSKRVLQ  195 (196)
Q Consensus       148 ~k~rR~RT~ft~~Ql~~L~~~F~~~~~p~~~~r~~La~~l---------------------gL~~~~Vq  195 (196)
                      ++.||.||.|+..|+.+|+..|+.++||+...|++||..+                     .|++.+|+
T Consensus         4 ~~~Rr~Rt~ft~~ql~~Le~~F~~~~yPs~~~Re~LA~~ln~~~c~q~g~~~~~~~GL~~~~lte~~V~   72 (102)
T 2da6_A            4 GSSGRNRFKWGPASQQILYQAYDRQKNPSKEEREALVEECNRAECLQRGVSPSKAHGLGSNLVTEVRVY   72 (102)
T ss_dssp             CCSCCCCCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHHHHHHHHTSCCTTCGGGGGGGCCCHHHHH
T ss_pred             CCCCCCCccCCHHHHHHHHHHHcCCCCCCHHHHHHHHHHHHHhhhcccccccchhccccccccccccee
Confidence            4678899999999999999999999999999999999999                     78888886

>1lfb_A Liver transcription factor (LFB1); transcription regulation; 2.80A {Rattus norvegicus} SCOP: a.4.1.1 PDB: 2lfb_A

Probab=98.83  E-value=1.7e-09  Score=77.17  Aligned_cols=50  Identities=12%  Similarity=0.280  Sum_probs=40.9

Q ss_pred             cccccchhhcccchhhHhhhhhhhcccCCCChHHHHHHHHH------------------hC---cchhhhc
Q psy17504        146 SHQRTKRMRTSFKHHQLRTMKSYFNINQNPDAKDLKQLAQK------------------TG---LSKRVLQ  195 (196)
Q Consensus       146 ~~~k~rR~RT~ft~~Ql~~L~~~F~~~~~p~~~~r~~La~~------------------lg---L~~~~Vq  195 (196)
                      ..++.||.||.|+..|+..|+..|+.++||+...|++||..                  +|   |++.+|+
T Consensus         5 ~~~k~rr~Rt~ft~~Ql~~LE~~F~~~~yP~~~~R~eLA~~~n~~~~~~~g~~~~~~~~lg~~~lse~qV~   75 (99)
T 1lfb_A            5 PTKKGRRNRFKWGPASQQILFQAYERQKNPSKEERETLVEECNRAECIQRGVSPSQAQGLGSNLVTEVRVY   75 (99)
T ss_dssp             --------CCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHHHHHHTTTTCCTTCTTTTGGGCCCHHHHH
T ss_pred             CCCCCCCCCcCcCHHHHHHHHHHHhcCCCCCHHHHHHHHHHhccccccccccccccccccCccccCcceee
Confidence            34577889999999999999999999999999999999999                  88   9999986

>2dar_A PDZ and LIM domain protein 5; enigma homolog protein, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: g.39.1.3 g.39.1.3

Probab=98.83  E-value=9.4e-11  Score=81.85  Aligned_cols=47  Identities=21%  Similarity=0.323  Sum_probs=41.5

Q ss_pred             HHHHHhHHHhhhhhhhhhhcceeccCCccccccceeeeccchhhhhhc
Q psy17504          9 VMRARDLVFHLHCFTCISCGILLTKGDLFGMRDEMIYCRPHYEILRHR   56 (196)
Q Consensus         9 v~~a~~~~~H~~CF~C~~C~~~L~~G~~f~~~~~~~~C~~~y~~~~~~   56 (196)
                      ++.|.++.||..||+|..|+++|. +..|...++++||+.||..++..
T Consensus        39 ~v~a~~~~~H~~CF~C~~C~~~L~-~~~f~~~~g~~yC~~cy~~~f~~   85 (90)
T 2dar_A           39 FLVALGKSWHPEEFNCAHCKNTMA-YIGFVEEKGALYCELCYEKFFAS   85 (90)
T ss_dssp             EEEETTEEECTTTCBCSSSCCBCS-SSCBEESSSCEECHHHHHHHTSC
T ss_pred             EEEECCccccccCCccCCCCCCCC-CCEeEeECCEEECHHHHHHHcCC
Confidence            456889999999999999999994 66788899999999999998853

>2d8y_A Eplin protein; LIM domain, epithelial protein LOST in neoplasm, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: g.39.1.3 g.39.1.3

Probab=98.82  E-value=7.7e-11  Score=82.47  Aligned_cols=52  Identities=33%  Similarity=0.698  Sum_probs=43.4

Q ss_pred             CChHHHHHHHHhHHHhhhhhhhhhhcceeccCCccccccceeeeccchhhhhhc
Q psy17504          3 ISSSELVMRARDLVFHLHCFTCISCGILLTKGDLFGMRDEMIYCRPHYEILRHR   56 (196)
Q Consensus         3 i~~~~~v~~a~~~~~H~~CF~C~~C~~~L~~G~~f~~~~~~~~C~~~y~~~~~~   56 (196)
                      |.+.++| .|.++.||..||+|..|+++|..+ .|...++++||+.||..++..
T Consensus        25 I~~~~~v-~a~~~~~H~~CF~C~~C~~~L~~~-~~~~~~g~~yC~~~y~~~f~~   76 (91)
T 2d8y_A           25 VYPMERL-LANQQVFHISCFRCSYCNNKLSLG-TYASLHGRIYCKPHFNQLFKS   76 (91)
T ss_dssp             CCTTSEE-ECSSSEEETTTCBCTTTCCBCCTT-TCCCSSSCCCCHHHHHHHSCC
T ss_pred             cCCceeE-EECCCEECCCCCeeCCCCCCCCCC-CcEeECCEEECHHHHHHHhCC
Confidence            4444544 789999999999999999999554 477889999999999998864

>1a7i_A QCRP2 (LIM1); LIM domain containing proteins, metal-binding protein, zinc finger; NMR {Coturnix japonica} SCOP: g.39.1.3 g.39.1.3 PDB: 2o10_A

Probab=98.81  E-value=8.4e-11  Score=80.40  Aligned_cols=52  Identities=23%  Similarity=0.523  Sum_probs=42.9

Q ss_pred             CChHHHHHHHHhHHHhhhhhhhhhhcceeccCCccccccceeeeccchhhhhhc
Q psy17504          3 ISSSELVMRARDLVFHLHCFTCISCGILLTKGDLFGMRDEMIYCRPHYEILRHR   56 (196)
Q Consensus         3 i~~~~~v~~a~~~~~H~~CF~C~~C~~~L~~G~~f~~~~~~~~C~~~y~~~~~~   56 (196)
                      |.+.+ ++.+.++.||..||+|..|+++|. +..|..+++++||+.||..++..
T Consensus        17 I~~~~-~~~a~~~~~H~~CF~C~~C~~~L~-~~~~~~~~~~~yC~~cy~~~f~~   68 (81)
T 1a7i_A           17 VYHAE-EVQCDGRSFHRCCFLCMVCRKNLD-STTVAIHDAEVYCKSCYGKKYGP   68 (81)
T ss_dssp             CSSTT-EEEETTEEEESSSEECSSSCCEEC-SSCCEEETTEEECSHHHHHHCC-
T ss_pred             ccCce-eEEeCCcccccccCccCCCCCCCC-CCCeEeeCCEEECHHHHHHHhCC
Confidence            44444 357889999999999999999994 45688889999999999988754

>2dmn_A Homeobox protein TGIF2LX; TGFB-induced factor 2-like protein, X-linked TGF(beta) induced transcription factor 2-like protein, TGIF-like on the X; NMR {Homo sapiens}

Probab=98.80  E-value=2e-09  Score=74.25  Aligned_cols=48  Identities=17%  Similarity=0.337  Sum_probs=44.1

Q ss_pred             ccchhhcccchhhHhhhhhhhcc---cCCCChHHHHHHHHHhCcchhhhcC
Q psy17504        149 RTKRMRTSFKHHQLRTMKSYFNI---NQNPDAKDLKQLAQKTGLSKRVLQN  196 (196)
Q Consensus       149 k~rR~RT~ft~~Ql~~L~~~F~~---~~~p~~~~r~~La~~lgL~~~~Vq~  196 (196)
                      +.|+.|+.|+..|+..|+..|..   ++||+..+|++||..+||++.||++
T Consensus         6 ~~rk~R~~~s~~q~~~L~~~f~~~~~~pYPs~~~r~~LA~~~gLs~~qV~~   56 (83)
T 2dmn_A            6 SGKKRKGNLPAESVKILRDWMYKHRFKAYPSEEEKQMLSEKTNLSLLQISN   56 (83)
T ss_dssp             CCCCCCSSCCHHHHHHHHHHHHHTTTTCCCCHHHHHHHHHHHCCCHHHHHH
T ss_pred             CCCCCCCcCCHHHHHHHHHHHHHhccCCCCCHHHHHHHHHHHCcCHHHhhH
Confidence            56778999999999999999877   6999999999999999999999973

>1uhs_A HOP, homeodomain only protein; structural genomics, cardiac development, riken structural genomics/proteomics initiative, RSGI, transcription; NMR {Mus musculus} SCOP: a.4.1.1

Probab=98.80  E-value=2.8e-09  Score=71.48  Aligned_cols=44  Identities=25%  Similarity=0.409  Sum_probs=42.0

Q ss_pred             hhhcccchhhHhhhhhhhcc-cCCCChHHHHHHHHHhCcchhhhc
Q psy17504        152 RMRTSFKHHQLRTMKSYFNI-NQNPDAKDLKQLAQKTGLSKRVLQ  195 (196)
Q Consensus       152 R~RT~ft~~Ql~~L~~~F~~-~~~p~~~~r~~La~~lgL~~~~Vq  195 (196)
                      +.||.|+..|+..|+..|.. ++||+...+++||..+||++.+||
T Consensus         3 k~Rt~ft~~Q~~~Le~~F~~~~~yp~~~~r~~LA~~l~l~~~qV~   47 (72)
T 1uhs_A            3 EGAATMTEDQVEILEYNFNKVNKHPDPTTLCLIAAEAGLTEEQTQ   47 (72)
T ss_dssp             CCCCCCCHHHHHHHHHHHHSSCSSCCHHHHHHHHHHHTCCHHHHH
T ss_pred             CCCccCCHHHHHHHHHHHHccCCCCCHHHHHHHHHHHCcCHHHhh
Confidence            46899999999999999996 999999999999999999999997

>2dj7_A Actin-binding LIM protein 3; LIM domain, Zn binding protein, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: g.39.1.3 g.39.1.3

Probab=98.79  E-value=2.4e-10  Score=78.30  Aligned_cols=45  Identities=31%  Similarity=0.720  Sum_probs=40.0

Q ss_pred             HHHHhHHHhhhhhhhhhhcceeccCCccccccceeeeccchhhhhhc
Q psy17504         10 MRARDLVFHLHCFTCISCGILLTKGDLFGMRDEMIYCRPHYEILRHR   56 (196)
Q Consensus        10 ~~a~~~~~H~~CF~C~~C~~~L~~G~~f~~~~~~~~C~~~y~~~~~~   56 (196)
                      +.|.++.||..||+|..|+++|. + .|+.+++++||+.||..+|..
T Consensus        31 v~a~~~~wH~~CF~C~~C~~~L~-~-~~~~~~g~~yC~~~y~~~fg~   75 (80)
T 2dj7_A           31 LLALDKQWHVSCFKCQTCSVILT-G-EYISKDGVPYCESDYHAQFGS   75 (80)
T ss_dssp             EEETTEEECTTTCBCSSSCCBCS-S-CCEEETTEEECTTHHHHHTTC
T ss_pred             EEECCcccccccCCcCcCCCCcC-C-CeEEECCEEECHHHHHHHcCC
Confidence            46789999999999999999995 5 688899999999999998853

>1puf_B PRE-B-cell leukemia transcription factor-1; homeodomian, protein-DNA complex, HOX hexapeptide, TALE homeodomain, homeodomain interaction; 1.90A {Homo sapiens} SCOP: a.4.1.1 PDB: 1b8i_B* 2r5y_B* 2r5z_B*

Probab=98.79  E-value=2.5e-09  Score=71.83  Aligned_cols=46  Identities=26%  Similarity=0.501  Sum_probs=43.7

Q ss_pred             chhhcccchhhHhhhhhhh---cccCCCChHHHHHHHHHhCcchhhhcC
Q psy17504        151 KRMRTSFKHHQLRTMKSYF---NINQNPDAKDLKQLAQKTGLSKRVLQN  196 (196)
Q Consensus       151 rR~RT~ft~~Ql~~L~~~F---~~~~~p~~~~r~~La~~lgL~~~~Vq~  196 (196)
                      ||.||.|+..|+..|+..|   ..++||+...++.||..+||++.+|++
T Consensus         2 rr~R~~ft~~q~~~Le~~f~~~~~~~yP~~~~r~~La~~~~L~~~qV~~   50 (73)
T 1puf_B            2 RRKRRNFNKQATEILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSN   50 (73)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHHTTTSCCCCHHHHHHHHHHHTSCHHHHHH
T ss_pred             CCCCCcCCHHHHHHHHHHHHHhccCCCcCHHHHHHHHHHHCcCHHHHHH
Confidence            6789999999999999999   999999999999999999999999973

>2cuq_A Four and A half LIM domains 3; structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: g.39.1.3 g.39.1.3

Probab=98.78  E-value=1.7e-10  Score=78.60  Aligned_cols=46  Identities=33%  Similarity=0.590  Sum_probs=41.8

Q ss_pred             HHHHHhHHHhhhhhhhhhhcceeccCCccccccceeeeccchhhhhh
Q psy17504          9 VMRARDLVFHLHCFTCISCGILLTKGDLFGMRDEMIYCRPHYEILRH   55 (196)
Q Consensus         9 v~~a~~~~~H~~CF~C~~C~~~L~~G~~f~~~~~~~~C~~~y~~~~~   55 (196)
                      +++|.++.||..||+|..|+++| .+..|.+.++++||+.||..++.
T Consensus        29 ~v~a~~~~~H~~CF~C~~C~~~L-~~~~~~~~~~~~yC~~cy~~~f~   74 (80)
T 2cuq_A           29 GVTYRDQPWHRECLVCTGCQTPL-AGQQFTSRDEDPYCVACFGELFA   74 (80)
T ss_dssp             CEESSSSEECTTTCBCSSSCCBC-TTCCEEECSSSEEEHHHHHHHTT
T ss_pred             EEEECCchhhhhhCCcccCCCcC-CCCeeEeECCEEECHHHHHHHcC
Confidence            56789999999999999999999 57788889999999999998875

>2cor_A Pinch protein; LIM domain, particularly interesting NEW Cys- His protein, LIM and senescent cell antigen-like domains 1, structural genomics; NMR {Homo sapiens} SCOP: g.39.1.3 g.39.1.3

Probab=98.78  E-value=1.2e-10  Score=79.48  Aligned_cols=46  Identities=24%  Similarity=0.430  Sum_probs=39.8

Q ss_pred             HHHHHHhHHHhhhhhhhhhhcceeccCCccccccceeeeccchhhhhh
Q psy17504          8 LVMRARDLVFHLHCFTCISCGILLTKGDLFGMRDEMIYCRPHYEILRH   55 (196)
Q Consensus         8 ~v~~a~~~~~H~~CF~C~~C~~~L~~G~~f~~~~~~~~C~~~y~~~~~   55 (196)
                      .++.|.++.||..||+|..|+++|. +..| .+++++||..||..++.
T Consensus        28 ~~v~a~~~~~H~~CF~C~~C~~~L~-~~~f-~~~g~~yC~~cy~~~f~   73 (79)
T 2cor_A           28 QPLIFKNDPYHPDHFNCANCGKELT-ADAR-ELKGELYCLPCHDKMGV   73 (79)
T ss_dssp             CCCCCSSSCCCTTTSBCSSSCCBCC-TTCE-EETTEEECHHHHHTTSC
T ss_pred             eEEEECcceeCCCCCEeCCCCCccC-CCCE-eECCEEeCHHHHHHhCC
Confidence            4567899999999999999999995 4455 78999999999998875

>2da5_A Zinc fingers and homeoboxes protein 3; homeobox domain, three helices with the DNA binding helix- turn-helix motif, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=98.77  E-value=3.9e-09  Score=71.39  Aligned_cols=43  Identities=26%  Similarity=0.369  Sum_probs=40.7

Q ss_pred             hhcccchhhHhhhhhhhcccCCCChHHHHHHHHHhCcchhhhc
Q psy17504        153 MRTSFKHHQLRTMKSYFNINQNPDAKDLKQLAQKTGLSKRVLQ  195 (196)
Q Consensus       153 ~RT~ft~~Ql~~L~~~F~~~~~p~~~~r~~La~~lgL~~~~Vq  195 (196)
                      .|+.||..|+..|+..|..++||+...+++||..+||++.+|+
T Consensus        10 kr~~~t~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~   52 (75)
T 2da5_A           10 KYKERAPEQLRALESSFAQNPLPLDEELDRLRSETKMTRREID   52 (75)
T ss_dssp             CCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHCCCHHHHH
T ss_pred             CCccCCHHHHHHHHHHHhccCCCCHHHHHHHHHHhCCCHHHhh
Confidence            4567999999999999999999999999999999999999997

>3a03_A T-cell leukemia homeobox protein 2; homeodomain, developmental protein, DNA-binding, N gene regulation; 1.54A {Homo sapiens}

Probab=98.76  E-value=4e-09  Score=67.29  Aligned_cols=41  Identities=17%  Similarity=0.229  Sum_probs=38.4

Q ss_pred             cccchhhHhhhhhhhcccCCCChHHHHHHHHHhCcchhhhc
Q psy17504        155 TSFKHHQLRTMKSYFNINQNPDAKDLKQLAQKTGLSKRVLQ  195 (196)
Q Consensus       155 T~ft~~Ql~~L~~~F~~~~~p~~~~r~~La~~lgL~~~~Vq  195 (196)
                      |.||..|+..|+..|..++||+...|++||..+||++.+||
T Consensus         2 T~ft~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~   42 (56)
T 3a03_A            2 TSFSRSQVLELERRFLRQKYLASAERAALAKALRMTDAQVK   42 (56)
T ss_dssp             --CCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHH
T ss_pred             CccCHHHHHHHHHHHHhcCCcCHHHHHHHHHHhCcCHHHhh
Confidence            78999999999999999999999999999999999999997

>1iml_A CRIP, cysteine rich intestinal protein; metal-binding protein, LIM domain protein; NMR {Rattus rattus} SCOP: g.39.1.3 g.39.1.3

Probab=98.76  E-value=3e-10  Score=76.66  Aligned_cols=52  Identities=23%  Similarity=0.446  Sum_probs=42.9

Q ss_pred             CChHHHHHHHHhHHHhhhhhhhhhhcceeccCCccccccceeeec-cchhhhhhc
Q psy17504          3 ISSSELVMRARDLVFHLHCFTCISCGILLTKGDLFGMRDEMIYCR-PHYEILRHR   56 (196)
Q Consensus         3 i~~~~~v~~a~~~~~H~~CF~C~~C~~~L~~G~~f~~~~~~~~C~-~~y~~~~~~   56 (196)
                      |.+.+. +.|.++.||..||+|..|+++|.. ..|...++++||+ .||..++..
T Consensus        10 I~~~~~-v~a~~~~~H~~CF~C~~C~~~L~~-~~~~~~~g~~yC~~~cy~~~f~~   62 (76)
T 1iml_A           10 VYFAER-VTSLGKDWHRPCLKCEKCGKTLTS-GGHAEHEGKPYCNHPCYSAMFGP   62 (76)
T ss_dssp             CCGGGE-EEETTEEEETTTCBCTTTCCBCCT-TTEEEETTEEEETTTHHHHHSSC
T ss_pred             EECceE-EEECCccccCCCCCccccCccCCC-CceECcCCeEeeCHHHHHHHhCc
Confidence            444544 467899999999999999999954 4788899999999 699988753

>2iyb_E Testin, TESS, TES; LIM domain, SH3-binding, tumour supressor LIM domain EVH1 DO cell motility, phosphorylation, cytoskeleton; 2.35A {Homo sapiens}

Probab=98.75  E-value=1e-10  Score=76.79  Aligned_cols=50  Identities=22%  Similarity=0.496  Sum_probs=41.9

Q ss_pred             CChHHHHHHHHhHHHh--hhhhhhhhhcceeccCCccccccceeee-ccchhhh
Q psy17504          3 ISSSELVMRARDLVFH--LHCFTCISCGILLTKGDLFGMRDEMIYC-RPHYEIL   53 (196)
Q Consensus         3 i~~~~~v~~a~~~~~H--~~CF~C~~C~~~L~~G~~f~~~~~~~~C-~~~y~~~   53 (196)
                      |.+.+.++.|.++.||  ..||+|..|+++| .|..|..+++++|| ..+|..+
T Consensus        12 I~~~~~~v~a~~~~wH~~~~CF~C~~C~~~L-~~~~f~~~~g~~yC~~~C~~k~   64 (65)
T 2iyb_E           12 IDPEVQRVTYNNFSWHASTECFLCSCCSKCL-IGQKFMPVEGMVFCSVECKKRM   64 (65)
T ss_dssp             ECTTSCEEEETTEEEETTTTTSBCTTTCCBC-TTSCCEEETTEEESSHHHHHTT
T ss_pred             eccCceEEEECCCccCCCCCCEECCCCCCcC-CCCceEEECCEEecCHHHhhhh
Confidence            3444456788999999  9999999999999 67789999999999 7777654

>1e3o_C Octamer-binding transcription factor 1; transcription factor, POU domain, dimer, DNA binding; 1.9A {Homo sapiens} SCOP: a.4.1.1 a.35.1.1 PDB: 1gt0_C 1hf0_A* 1cqt_A* 1o4x_A 1oct_C* 1pou_A 1pog_A 1hdp_A

Probab=98.75  E-value=3.6e-09  Score=81.68  Aligned_cols=48  Identities=25%  Similarity=0.452  Sum_probs=42.3

Q ss_pred             cccchhhcccchhhHhhhhhhhcccCCCChHHHHHHHHHhCcchhhhc
Q psy17504        148 QRTKRMRTSFKHHQLRTMKSYFNINQNPDAKDLKQLAQKTGLSKRVLQ  195 (196)
Q Consensus       148 ~k~rR~RT~ft~~Ql~~L~~~F~~~~~p~~~~r~~La~~lgL~~~~Vq  195 (196)
                      .++||.||.|+..|+..|+..|..++||+...|++||..+||++++||
T Consensus        99 ~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~L~~~qV~  146 (160)
T 1e3o_C           99 SRRRKKRTSIETNIRVALEKSFMENQKPTSEDITLIAEQLNMEKEVIR  146 (160)
T ss_dssp             -----CCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHH
T ss_pred             CCCCcCccccCHHHHHHHHHHHhhcCCCCHHHHHHHHHHHCCChHHhh
Confidence            467889999999999999999999999999999999999999999997

>1au7_A Protein PIT-1, GHF-1; complex (DNA-binding protein/DNA), pituitary, CPHD, POU domain, transcription factor, transcription/DNA complex; HET: DNA; 2.30A {Rattus norvegicus} SCOP: a.4.1.1 a.35.1.1

Probab=98.75  E-value=3.6e-09  Score=80.55  Aligned_cols=49  Identities=18%  Similarity=0.428  Sum_probs=43.1

Q ss_pred             ccccchhhcccchhhHhhhhhhhcccCCCChHHHHHHHHHhCcchhhhc
Q psy17504        147 HQRTKRMRTSFKHHQLRTMKSYFNINQNPDAKDLKQLAQKTGLSKRVLQ  195 (196)
Q Consensus       147 ~~k~rR~RT~ft~~Ql~~L~~~F~~~~~p~~~~r~~La~~lgL~~~~Vq  195 (196)
                      .+++||.||.|+..|+..|+..|..++||+...|++||..+||++++||
T Consensus        84 ~~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~L~~~qV~  132 (146)
T 1au7_A           84 NERKRKRRTTISIAAKDALERHFGEHSKPSSQEIMRMAEELNLEKEVVR  132 (146)
T ss_dssp             -----CCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHH
T ss_pred             CCCCCCCCcCccHHHHHHHHHHHHHcCCCCHHHHHHHHHHhCCChhhch
Confidence            3466788999999999999999999999999999999999999999997

>2cup_A Skeletal muscle LIM-protein 1; four and half LIM domains protein 1, LIM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: g.39.1.3 g.39.1.3 g.39.1.3

Probab=98.75  E-value=1.1e-10  Score=82.94  Aligned_cols=52  Identities=21%  Similarity=0.408  Sum_probs=45.2

Q ss_pred             CChHHHHHHHHhHHHhhhhhhhhhhcceeccCCccccccceeeeccchhhhhh
Q psy17504          3 ISSSELVMRARDLVFHLHCFTCISCGILLTKGDLFGMRDEMIYCRPHYEILRH   55 (196)
Q Consensus         3 i~~~~~v~~a~~~~~H~~CF~C~~C~~~L~~G~~f~~~~~~~~C~~~y~~~~~   55 (196)
                      |.+.+.++.+.++.||..||+|..|+++| .+..|+..++++||+.||..++.
T Consensus        15 I~~~~~~~~a~~~~~H~~CF~C~~C~~~L-~~~~~~~~~g~~yC~~cy~~~~~   66 (101)
T 2cup_A           15 IGADSKEVHYKNRFWHDTCFRCAKCLHPL-ANETFVAKDNKILCNKCTTREDS   66 (101)
T ss_dssp             CCSSSCEEEETTEEEETTTCCCSSSCCCT-TSSCCEEETTEEECHHHHTTCCC
T ss_pred             ccCCceEEEECccChhhcCCcccccCCCC-CcCeeECcCCEEEChhHhhhhcC
Confidence            44445677889999999999999999999 67788889999999999988774

>3d1n_I POU domain, class 6, transcription factor 1; protein-DNA complex, helix-turn-helix (HTH), DNA-binding, homeobox, nucleus, transcription regulation; 2.51A {Homo sapiens}

Probab=98.74  E-value=4.3e-09  Score=80.44  Aligned_cols=48  Identities=21%  Similarity=0.556  Sum_probs=45.7

Q ss_pred             cccchhhcccchhhHhhhhhhhcccCCCChHHHHHHHHHhCcchhhhc
Q psy17504        148 QRTKRMRTSFKHHQLRTMKSYFNINQNPDAKDLKQLAQKTGLSKRVLQ  195 (196)
Q Consensus       148 ~k~rR~RT~ft~~Ql~~L~~~F~~~~~p~~~~r~~La~~lgL~~~~Vq  195 (196)
                      .++||.||.|+..|+..|+..|..++||+...|++||..+||++++||
T Consensus        91 ~~~rr~Rt~ft~~q~~~Le~~F~~~~yp~~~~r~~LA~~l~L~~~qV~  138 (151)
T 3d1n_I           91 SKKRKRRTSFTPQAIEALNAYFEKNPLPTGQEITEMAKELNYDREVVR  138 (151)
T ss_dssp             CCCCCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTSCHHHHH
T ss_pred             CCCCCCCcccCHHHHHHHHHHHHhcCCCCHHHHHHHHHHHCCCHHHhH
Confidence            467789999999999999999999999999999999999999999997

>2dlo_A Thyroid receptor-interacting protein 6; LIM domain, OPA-interacting protein 1, zyxin related protein 1 (ZRP-1), structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: g.39.1.3 g.39.1.3

Probab=98.74  E-value=2.6e-10  Score=77.92  Aligned_cols=47  Identities=28%  Similarity=0.509  Sum_probs=41.6

Q ss_pred             HHHHHHhHHHhhhhhhhhhhcceeccCCccccc-cceeeeccchhhhhh
Q psy17504          8 LVMRARDLVFHLHCFTCISCGILLTKGDLFGMR-DEMIYCRPHYEILRH   55 (196)
Q Consensus         8 ~v~~a~~~~~H~~CF~C~~C~~~L~~G~~f~~~-~~~~~C~~~y~~~~~   55 (196)
                      .+++|.++.||..||+|..|+++| .+..|.+. ++++||+.||..++.
T Consensus        28 ~~~~a~~~~~H~~CF~C~~C~~~L-~~~~f~~~~~g~~yC~~cy~~~f~   75 (81)
T 2dlo_A           28 RILRAMGKAYHPGCFTCVVCHRGL-DGIPFTVDATSQIHCIEDFHRKFA   75 (81)
T ss_dssp             CCEEETTEEECTTTCBCSSSCCBC-TTSCEECCTTCCCEEHHHHHHHTT
T ss_pred             eeEEECCccccHHhcCcccCCCcc-CCCeeEECCCCEEECHHHHHHHhc
Confidence            467889999999999999999999 47788776 789999999998875

>1b72_B Protein (PBX1); homeodomain, DNA, complex, DNA-binding protein, protein/DNA complex; HET: DNA; 2.35A {Homo sapiens} SCOP: a.4.1.1 PDB: 1lfu_P

Probab=98.74  E-value=4.5e-09  Score=72.91  Aligned_cols=46  Identities=26%  Similarity=0.501  Sum_probs=43.1

Q ss_pred             chhhcccchhhHhhhhhhh---cccCCCChHHHHHHHHHhCcchhhhcC
Q psy17504        151 KRMRTSFKHHQLRTMKSYF---NINQNPDAKDLKQLAQKTGLSKRVLQN  196 (196)
Q Consensus       151 rR~RT~ft~~Ql~~L~~~F---~~~~~p~~~~r~~La~~lgL~~~~Vq~  196 (196)
                      ||.||.|+..|+..|+..|   ..++||+..++++||..+||++.+|++
T Consensus         2 rr~R~~ft~~q~~~Le~~f~~h~~~~yp~~~~r~~La~~~~l~~~qV~~   50 (87)
T 1b72_B            2 RRKRRNFNKQATEILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSN   50 (87)
T ss_dssp             -CCCCCCCHHHHHHHHHHHHTTTTSCCCCHHHHHHHHHHHTSCHHHHHH
T ss_pred             CCCCCCCCHHHHHHHHHHHHHhccCCCCCHHHHHHHHHHHCcCHHHHHH
Confidence            6789999999999999999   999999999999999999999999973

>1x3h_A Leupaxin; paxillin family, protein-protein interaction, LIM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: g.39.1.3 g.39.1.3

Probab=98.74  E-value=2.8e-10  Score=77.49  Aligned_cols=46  Identities=30%  Similarity=0.529  Sum_probs=40.8

Q ss_pred             HHHHHhHHHhhhhhhhhhhcceeccCCccccccceeeeccchhhhhh
Q psy17504          9 VMRARDLVFHLHCFTCISCGILLTKGDLFGMRDEMIYCRPHYEILRH   55 (196)
Q Consensus         9 v~~a~~~~~H~~CF~C~~C~~~L~~G~~f~~~~~~~~C~~~y~~~~~   55 (196)
                      +++|.++.||..||+|..|+++|.. ..|...++++||+.||..++.
T Consensus        29 ~v~a~~~~~H~~CF~C~~C~~~L~~-~~~~~~~~~~yC~~~y~~~f~   74 (80)
T 1x3h_A           29 YLSAMDTVWHPECFVCGDCFTSFST-GSFFELDGRPFCELHYHHRRG   74 (80)
T ss_dssp             CEEETTEEECTTTCBCSSSCCBSCS-SCCEESSSCEECHHHHHHHHS
T ss_pred             eEEECCCeEecCcCChhhCCCCCCC-CcEEeECCEEECHHHHHHHcC
Confidence            4678999999999999999999954 468888999999999998875

>1rut_X Flinc4, fusion protein of LMO4 protein and LIM domain- binding protein 1; B-tandem zipper, protein binding; 1.30A {Mus musculus} SCOP: g.39.1.3 g.39.1.3 g.39.1.3 g.39.1.3 PDB: 2dfy_X 2xjz_I 2xjy_B

Probab=98.73  E-value=2.5e-10  Score=90.14  Aligned_cols=54  Identities=39%  Similarity=0.691  Sum_probs=47.4

Q ss_pred             CChHHHHHHHHhHHHhhhhhhhhhhcceeccCCccccccceeeeccchhhhhhc
Q psy17504          3 ISSSELVMRARDLVFHLHCFTCISCGILLTKGDLFGMRDEMIYCRPHYEILRHR   56 (196)
Q Consensus         3 i~~~~~v~~a~~~~~H~~CF~C~~C~~~L~~G~~f~~~~~~~~C~~~y~~~~~~   56 (196)
                      |.+.+.+++|.++.||..||+|..|+++|..|+.|++.++++||+.||..++..
T Consensus        79 I~~~e~~i~a~~~~~H~~CF~C~~C~~~L~~g~~f~~~~g~~yC~~c~~~~~~~  132 (188)
T 1rut_X           79 IPASELVMRAQGNVYHLKCFTCSTCRNRLVPGDRFHYINGSLFCEHDRPTALIN  132 (188)
T ss_dssp             ECTTSEEEEETTEEECGGGCBCTTTCCBCCTTCEEEEETTEEEEGGGCCTTTC-
T ss_pred             cccCcEEEEcCCCEEeCCCCeECCCCCCCCCCCeEEEECCeEECHHHHHHHhcc
Confidence            555667888999999999999999999997788999999999999999887653

>1j2o_A FLIN2, fusion of rhombotin-2 and LIM domain-binding protein 1; LIM-interaction-domain (LID), metal binding protein; NMR {Mus musculus} SCOP: g.39.1.3 g.39.1.3

Probab=98.73  E-value=2.9e-10  Score=82.82  Aligned_cols=49  Identities=27%  Similarity=0.478  Sum_probs=43.5

Q ss_pred             HHHHHhHHHhhhhhhhhhhcceecc-CCccccccceeeeccchhhhhhcc
Q psy17504          9 VMRARDLVFHLHCFTCISCGILLTK-GDLFGMRDEMIYCRPHYEILRHRD   57 (196)
Q Consensus         9 v~~a~~~~~H~~CF~C~~C~~~L~~-G~~f~~~~~~~~C~~~y~~~~~~~   57 (196)
                      +++|.++.||..||+|..|+++|.. |..|+.+++++||+.||..+|...
T Consensus        18 ~~~a~~~~wH~~CF~C~~C~~~L~~~g~~~~~~~g~~yC~~~y~~~f~~~   67 (114)
T 1j2o_A           18 FLKAIDQYWHEDCLSCDLCGCRLGEVGRRLYYKLGRKLCRRDYLRLGGSG   67 (114)
T ss_dssp             EEECSSSEECTTTCCCSSSCSCCCCSSSCCCCBTTBCCCHHHHHHHHTSC
T ss_pred             EEEECchhHHHhcCcccccCCchhcCCCeeEEECCeeechHHHHHHhCcc
Confidence            5678899999999999999999963 678889999999999999998754

>1mnm_C Protein (MAT alpha-2 transcriptional repressor); transcription regulation, transcriptional repression, DNA- binding protein; HET: DNA; 2.25A {Saccharomyces cerevisiae} SCOP: a.4.1.1

Probab=98.73  E-value=4.9e-09  Score=72.85  Aligned_cols=48  Identities=27%  Similarity=0.417  Sum_probs=44.3

Q ss_pred             ccchhhcccchhhHhhhhhhhcc---cCCCChHHHHHHHHHhCcchhhhcC
Q psy17504        149 RTKRMRTSFKHHQLRTMKSYFNI---NQNPDAKDLKQLAQKTGLSKRVLQN  196 (196)
Q Consensus       149 k~rR~RT~ft~~Ql~~L~~~F~~---~~~p~~~~r~~La~~lgL~~~~Vq~  196 (196)
                      ++++.||.|+..|+..|+..|..   ++||+..++++||..+||++.+|++
T Consensus        26 ~~~k~r~~ft~~q~~~Le~~f~~~~~~~yP~~~~r~~La~~~gL~~~qV~~   76 (87)
T 1mnm_C           26 TKPYRGHRFTKENVRILESWFAKNIENPYLDTKGLENLMKNTSLSRIQIKN   76 (87)
T ss_dssp             SSCCTTCCCCHHHHHHHHHHHHHTTSSCCCCHHHHHHHHHHHCCCHHHHHH
T ss_pred             CCCCCCCcCCHHHHHHHHHHHHHhCCCCCcCHHHHHHHHHHHCcCHHHHHH
Confidence            44556999999999999999999   9999999999999999999999973

>2xsd_C POU domain, class 3, transcription factor 1; transcription-DNA complex, SOX; 2.05A {Mus musculus}

Probab=98.72  E-value=5.1e-09  Score=81.21  Aligned_cols=49  Identities=27%  Similarity=0.363  Sum_probs=38.5

Q ss_pred             ccccchhhcccchhhHhhhhhhhcccCCCChHHHHHHHHHhCcchhhhc
Q psy17504        147 HQRTKRMRTSFKHHQLRTMKSYFNINQNPDAKDLKQLAQKTGLSKRVLQ  195 (196)
Q Consensus       147 ~~k~rR~RT~ft~~Ql~~L~~~F~~~~~p~~~~r~~La~~lgL~~~~Vq  195 (196)
                      .+++||.||.|+..|+..|+..|..++||+...|++||..+||++++||
T Consensus        96 ~~~~rr~Rt~ft~~Ql~~LE~~F~~~~yp~~~~r~~LA~~l~L~~~qV~  144 (164)
T 2xsd_C           96 QGRKRKKRTSIEVGVKGALESHFLKCPKPSAHEITGLADSLQLEKEVVR  144 (164)
T ss_dssp             ----------CCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHH
T ss_pred             cccCCCCceeccHHHHHHHHHHHhcCCCCCHHHHHHHHHHHCCChhhhh
Confidence            3567889999999999999999999999999999999999999999997

>1v6g_A Actin binding LIM protein 2; LIM domain, zinc binding domain, ablim2, structural genomics, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: g.39.1.3 g.39.1.3

Probab=98.67  E-value=5.1e-10  Score=76.43  Aligned_cols=48  Identities=21%  Similarity=0.428  Sum_probs=41.3

Q ss_pred             HHHHHHhHHHhhhhhhhhhhcceeccCCccccccceeeeccchhhhhh
Q psy17504          8 LVMRARDLVFHLHCFTCISCGILLTKGDLFGMRDEMIYCRPHYEILRH   55 (196)
Q Consensus         8 ~v~~a~~~~~H~~CF~C~~C~~~L~~G~~f~~~~~~~~C~~~y~~~~~   55 (196)
                      .+++|.++.||..||+|..|+++|..|..|.+.+..+||+.||..++.
T Consensus        28 ~~v~a~~~~wH~~CF~C~~C~~~L~~~~~~~~~~~~~~C~~C~~~~~~   75 (81)
T 1v6g_A           28 EVVSALGKTYHPDCFVCAVCRLPFPPGDRVTFNGKECMCQKCSLPVSV   75 (81)
T ss_dssp             CCEEETTEEECTTTSSCSSSCCCCCSSSCEEEETTEEEEHHHHSCCSS
T ss_pred             ceEEECCceeCccCCccccCCCCCCCCCEEEeCCCCEEChhhhcccCC
Confidence            467889999999999999999999778777766667899999987754

>2d5v_A Hepatocyte nuclear factor 6; transcription factor, transcription-DNA complex; 2.00A {Rattus norvegicus} PDB: 1s7e_A

Probab=98.67  E-value=8.9e-09  Score=79.61  Aligned_cols=50  Identities=26%  Similarity=0.369  Sum_probs=42.7

Q ss_pred             ccccchhhcccchhhHhhhhhhhcccCCCChHHHHHHHHHhCcchhhhcC
Q psy17504        147 HQRTKRMRTSFKHHQLRTMKSYFNINQNPDAKDLKQLAQKTGLSKRVLQN  196 (196)
Q Consensus       147 ~~k~rR~RT~ft~~Ql~~L~~~F~~~~~p~~~~r~~La~~lgL~~~~Vq~  196 (196)
                      ..+.||.||.|+..|+..|+..|+.++||+...|++||..+||++.+||+
T Consensus        94 ~~~~rr~Rt~ft~~q~~~Le~~F~~~~yp~~~~r~~la~~l~L~~~qV~~  143 (164)
T 2d5v_A           94 GNTPKKPRLVFTDVQRRTLHAIFKENKRPSKELQITISQQLGLELSTVSN  143 (164)
T ss_dssp             ------CCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHH
T ss_pred             CCCCCCCCCcCCHHHHHHHHHHHhcCCCCCHHHHHHHHHHHCcCHHHhhh
Confidence            34678899999999999999999999999999999999999999999973

>1k61_A Mating-type protein alpha-2; protein-DNA complex, homeodomain, hoogsteen base PAIR, transcription/DNA complex; HET: 5IU; 2.10A {Synthetic} SCOP: a.4.1.1

Probab=98.66  E-value=1e-08  Score=66.13  Aligned_cols=43  Identities=30%  Similarity=0.498  Sum_probs=41.1

Q ss_pred             hcccchhhHhhhhhhhcc---cCCCChHHHHHHHHHhCcchhhhcC
Q psy17504        154 RTSFKHHQLRTMKSYFNI---NQNPDAKDLKQLAQKTGLSKRVLQN  196 (196)
Q Consensus       154 RT~ft~~Ql~~L~~~F~~---~~~p~~~~r~~La~~lgL~~~~Vq~  196 (196)
                      |+.|+..|+..|+..|..   ++||+..++++||..+||++.+|++
T Consensus         2 r~~ft~~q~~~Le~~f~~~~~~~yp~~~~r~~La~~~gl~~~qV~~   47 (60)
T 1k61_A            2 GHRFTKENVRILESWFAKNIENPYLDTKGLENLMKNTSLSRIQIKN   47 (60)
T ss_dssp             CCSCCHHHHHHHHHHHHHTTTSCCCCHHHHHHHHHHHCCCHHHHHH
T ss_pred             cCcCCHHHHHHHHHHHHHcCCCCCcCHHHHHHHHHHHCcCHHHHHH
Confidence            689999999999999999   9999999999999999999999973

>1m3v_A FLIN4, fusion of the LIM interacting domain of LDB1 and the N-terminal LIM domain of LMO4...; fusion protein, LMO proteins, metal binding protein; NMR {Mus musculus} SCOP: g.39.1.3 g.39.1.3

Probab=98.65  E-value=6.5e-10  Score=81.90  Aligned_cols=48  Identities=31%  Similarity=0.510  Sum_probs=42.6

Q ss_pred             HHHHHhHHHhhhhhhhhhhcceec-cCCccccccceeeeccchhhhhhc
Q psy17504          9 VMRARDLVFHLHCFTCISCGILLT-KGDLFGMRDEMIYCRPHYEILRHR   56 (196)
Q Consensus         9 v~~a~~~~~H~~CF~C~~C~~~L~-~G~~f~~~~~~~~C~~~y~~~~~~   56 (196)
                      ++.|.++.||..||+|..|+++|. .|..|+.+++++||+.||..++..
T Consensus        20 ~~~a~~~~wH~~CF~C~~C~~~L~~~~~~~~~~~g~~yC~~cy~~~f~~   68 (122)
T 1m3v_A           20 LLYAMDSYWHSRCLKCSSCQAQLGDIGTSSYTKSGMILCRNDYIRLFGN   68 (122)
T ss_dssp             CEEETTEEECHHHHCCSSSCCCTTTSEECCEEETTEEECHHHHHHHHCC
T ss_pred             EEEECCceeHhhCCCcCCCCCcccccCCeEEEECCeeecHHHHHHHcCC
Confidence            456889999999999999999995 357788899999999999999865

>3l1p_A POU domain, class 5, transcription factor 1; POU, transcription factor DNA complex, pore, stem cells; HET: DNA; 2.80A {Mus musculus} PDB: 1ocp_A

Probab=98.63  E-value=1.6e-08  Score=77.56  Aligned_cols=48  Identities=27%  Similarity=0.463  Sum_probs=45.4

Q ss_pred             cccchhhcccchhhHhhhhhhhcccCCCChHHHHHHHHHhCcchhhhc
Q psy17504        148 QRTKRMRTSFKHHQLRTMKSYFNINQNPDAKDLKQLAQKTGLSKRVLQ  195 (196)
Q Consensus       148 ~k~rR~RT~ft~~Ql~~L~~~F~~~~~p~~~~r~~La~~lgL~~~~Vq  195 (196)
                      +++||.||.|+..|+..|+..|..++||+...|++||..+||++++||
T Consensus        94 ~~~rr~Rt~ft~~Q~~~Le~~F~~~~yps~~~r~~LA~~l~L~~~qV~  141 (155)
T 3l1p_A           94 QARKRKRTSIENRVRWSLETMFLKSPKPSLQQITHIANQLGLEKDVVR  141 (155)
T ss_dssp             CCSCCCCCCCCHHHHHHHHTTTTTCSCCCHHHHHHHHHHTTCCHHHHH
T ss_pred             cCCCCCCcccCHHHHHHHHHHHccCCCCCHHHHHHHHHHcCCChhhee
Confidence            356778999999999999999999999999999999999999999997

>2xqn_T Testin, TESS; metal-binding protein, cytoskeleton, focal adhesion, acrosom; 2.62A {Homo sapiens}

Probab=98.60  E-value=8.7e-10  Score=81.32  Aligned_cols=52  Identities=21%  Similarity=0.464  Sum_probs=46.1

Q ss_pred             CCChHHHHHHHHhHHHh--hhhhhhhhhcceeccCCccccccceeeeccchhhhh
Q psy17504          2 GISSSELVMRARDLVFH--LHCFTCISCGILLTKGDLFGMRDEMIYCRPHYEILR   54 (196)
Q Consensus         2 ~i~~~~~v~~a~~~~~H--~~CF~C~~C~~~L~~G~~f~~~~~~~~C~~~y~~~~   54 (196)
                      .|.+.+.+|++.+..||  ..||+|..|+++| .|+.|.+.++++||..||..++
T Consensus        72 ~I~~~~~~~~a~~~~~H~~~~CF~C~~C~~~l-~~~~f~~~~~~~yC~~~~~~~f  125 (126)
T 2xqn_T           72 AIDPEVQRVTYNNFSWHASTECFLCSCCSKCL-IGQKFMPVEGMVFCSVECKKRM  125 (126)
T ss_dssp             BCCTTSCEEEETTEEEESSTTTSBCTTTCCBC-TTSEEEEETTEEESSHHHHHSC
T ss_pred             cCCcCceEEECCCCEeeCCCCCcCcCCCCCcc-CCCeeEeECCEEcchHHhhhhc
Confidence            46666778899999999  9999999999999 4889999999999999998764

>1le8_B Mating-type protein alpha-2; matalpha2, isothermal titration calorimetry, protein-DNA complex, transcription/DNA complex; 2.30A {Saccharomyces cerevisiae} SCOP: a.4.1.1 PDB: 1akh_B* 1apl_C* 1yrn_B*

Probab=98.57  E-value=2.3e-08  Score=68.84  Aligned_cols=45  Identities=29%  Similarity=0.450  Sum_probs=41.1

Q ss_pred             hhhcccchhhHhhhhhhhcc---cCCCChHHHHHHHHHhCcchhhhcC
Q psy17504        152 RMRTSFKHHQLRTMKSYFNI---NQNPDAKDLKQLAQKTGLSKRVLQN  196 (196)
Q Consensus       152 R~RT~ft~~Ql~~L~~~F~~---~~~p~~~~r~~La~~lgL~~~~Vq~  196 (196)
                      +.|+.|+..|+..|+..|..   ++||+...+++||..+||++.+|++
T Consensus         4 krr~rft~~q~~~Le~~f~~h~~~~yP~~~~r~~La~~~gLt~~qV~~   51 (83)
T 1le8_B            4 YRGHRFTKENVRILESWFAKNIENPYLDTKGLENLMKNTSLSRIQIKN   51 (83)
T ss_dssp             -CCCCCCHHHHHHHHHHHHHTSSSCCCCHHHHHHHHHHHCCCHHHHHH
T ss_pred             CCCCCCCHHHHHHHHHHHHhhCCCCCcCHHHHHHHHHHHCCCHHHccc
Confidence            34566999999999999999   9999999999999999999999973

>2cqx_A LAG1 longevity assurance homolog 5; homeodomain, DNA binding domain, transcription, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: a.4.1.1

Probab=98.56  E-value=2.5e-08  Score=66.99  Aligned_cols=44  Identities=27%  Similarity=0.360  Sum_probs=40.4

Q ss_pred             hhhcccchhhHhhhhhhh-cccCCCChHHHHHHHHHhCcchhhhc
Q psy17504        152 RMRTSFKHHQLRTMKSYF-NINQNPDAKDLKQLAQKTGLSKRVLQ  195 (196)
Q Consensus       152 R~RT~ft~~Ql~~L~~~F-~~~~~p~~~~r~~La~~lgL~~~~Vq  195 (196)
                      +.|+.++..|+.+||..| ..++||+...|++||..+||++++||
T Consensus        10 k~r~r~~~~ql~~LE~~F~~~~~yp~~~~r~~LA~~l~l~e~qVq   54 (72)
T 2cqx_A           10 KDSPVNKVEPNDTLEKVFVSVTKYPDEKRLKGLSKQLDWSVRKIQ   54 (72)
T ss_dssp             CCCCCSCSCSTTHHHHHHHHTCSSCCHHHHHHHHHHTTCCHHHHH
T ss_pred             CCCCCCCHHHHHHHHHHHHhcCCCcCHHHHHHHHHHhCCChhhcc
Confidence            345567889999999999 99999999999999999999999997

>2xqn_T Testin, TESS; metal-binding protein, cytoskeleton, focal adhesion, acrosom; 2.62A {Homo sapiens}

Probab=98.56  E-value=2.5e-09  Score=78.86  Aligned_cols=46  Identities=26%  Similarity=0.629  Sum_probs=41.7

Q ss_pred             HHHHHhHHHhhhhhhhhhhcceeccCCccccccceeeeccchhhhhh
Q psy17504          9 VMRARDLVFHLHCFTCISCGILLTKGDLFGMRDEMIYCRPHYEILRH   55 (196)
Q Consensus         9 v~~a~~~~~H~~CF~C~~C~~~L~~G~~f~~~~~~~~C~~~y~~~~~   55 (196)
                      ++.|.++.||..||+|..|+++| .+..|+.+++++||+.||..++.
T Consensus        18 ~~~a~~~~~H~~CF~C~~C~~~L-~~~~f~~~~g~~yC~~cy~~~~~   63 (126)
T 2xqn_T           18 YTQAENQNWHLKHFCCFDCDSIL-AGEIYVMVNDKPVCKPCYVKNHA   63 (126)
T ss_dssp             EEEETTEEECGGGSBCTTTCCBC-TTSEEEEETTEEEEHHHHHHHSC
T ss_pred             EEeeCCCCccCCCCCcCCCCCCC-CcCEEEeECCEEechHHhCcCcC
Confidence            46788999999999999999999 57789899999999999998875

>2ecb_A Zinc fingers and homeoboxes protein 1; homeobox domain, transcription factor, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: a.4.1.1

Probab=98.54  E-value=3.8e-08  Score=68.72  Aligned_cols=40  Identities=23%  Similarity=0.335  Sum_probs=39.0

Q ss_pred             ccchhhHhhhhhhhcccCCCChHHHHHHHHHhCcchhhhc
Q psy17504        156 SFKHHQLRTMKSYFNINQNPDAKDLKQLAQKTGLSKRVLQ  195 (196)
Q Consensus       156 ~ft~~Ql~~L~~~F~~~~~p~~~~r~~La~~lgL~~~~Vq  195 (196)
                      .||..||.+|+..|..++||+...|++||..|||++++||
T Consensus        17 ~~t~~Ql~~Le~~F~~~~yp~~~~r~~LA~~lgLte~qVk   56 (89)
T 2ecb_A           17 EKTAEQLRVLQASFLNSSVLTDEELNRLRAQTKLTRREID   56 (89)
T ss_dssp             CCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTCCCHHHHH
T ss_pred             cCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCcChHHCe
Confidence            7899999999999999999999999999999999999997

>3nau_A Zinc fingers and homeoboxes protein 2; ZHX2, corepressor, homeodomain, domain swapping, structural oxford protein production facility, OPPF; 2.70A {Homo sapiens}

Probab=98.54  E-value=4e-08  Score=64.62  Aligned_cols=38  Identities=26%  Similarity=0.451  Sum_probs=36.5

Q ss_pred             chhhHhhhhhhhcccCCCChHHHHHHHHHhCcchhhhc
Q psy17504        158 KHHQLRTMKSYFNINQNPDAKDLKQLAQKTGLSKRVLQ  195 (196)
Q Consensus       158 t~~Ql~~L~~~F~~~~~p~~~~r~~La~~lgL~~~~Vq  195 (196)
                      |..||.+|+..|..++||+..+|++||..|||++++|+
T Consensus        12 ~~~Ql~~LE~~F~~~~YPs~~er~eLA~~tgLt~~qVk   49 (66)
T 3nau_A           12 TKEQIAHLKASFLQSQFPDDAEVYRLIEVTGLARSEIK   49 (66)
T ss_dssp             CHHHHHHHHHHHHGGGSCCHHHHHHHHHHHCCCHHHHH
T ss_pred             hHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCcCHHHhh
Confidence            56899999999999999999999999999999999997

>2dmp_A Zinc fingers and homeoboxes protein 2; homeobox domain, three helices with the DNA binding helix- turn-helix motif, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=98.53  E-value=6.7e-08  Score=67.44  Aligned_cols=40  Identities=23%  Similarity=0.347  Sum_probs=38.6

Q ss_pred             ccchhhHhhhhhhhcccCCCChHHHHHHHHHhCcchhhhc
Q psy17504        156 SFKHHQLRTMKSYFNINQNPDAKDLKQLAQKTGLSKRVLQ  195 (196)
Q Consensus       156 ~ft~~Ql~~L~~~F~~~~~p~~~~r~~La~~lgL~~~~Vq  195 (196)
                      .||..||.+|+..|..++||+...|++||..+||++++||
T Consensus        19 ~~t~~Ql~~Le~~F~~~~yp~~~~r~~La~~~~l~~~qV~   58 (89)
T 2dmp_A           19 EKTQGQVKILEDSFLKSSFPTQAELDRLRVETKLSRREID   58 (89)
T ss_dssp             CCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHH
T ss_pred             cCCHHHHHHHHHHHccCCCCCHHHHHHHHHHhCCCHHhcc
Confidence            3899999999999999999999999999999999999997

>2xjy_A Rhombotin-2; oncoprotein, T-cell leukemia, proto-oncogene, transcription, developmental protein; 2.40A {Homo sapiens} PDB: 2xjz_A

Probab=98.52  E-value=3.4e-09  Score=78.52  Aligned_cols=48  Identities=27%  Similarity=0.483  Sum_probs=42.4

Q ss_pred             HHHHHhHHHhhhhhhhhhhcceecc-CCccccccceeeeccchhhhhhc
Q psy17504          9 VMRARDLVFHLHCFTCISCGILLTK-GDLFGMRDEMIYCRPHYEILRHR   56 (196)
Q Consensus         9 v~~a~~~~~H~~CF~C~~C~~~L~~-G~~f~~~~~~~~C~~~y~~~~~~   56 (196)
                      ++.|.++.||..||+|..|+++|.. |..|+.+++++||+.||..++..
T Consensus        17 ~~~a~~~~wH~~CF~C~~C~~~L~~~~~~~~~~~g~~yC~~~y~~~~~~   65 (131)
T 2xjy_A           17 FLKAIDQYWHEDCLSCDLCGCRLGEVGRRLYYKLGRKLCRRDYLRLFGQ   65 (131)
T ss_dssp             EEEETTEEEETTTCBCTTTCCBCSSTTCCEEEETTEEECHHHHHHHHCC
T ss_pred             EEEECCCcccHHHcccCcCCCccccCCCeEEEECCEEeecCchhhhCCC
Confidence            4568899999999999999999963 67888899999999999998864

>2e19_A Transcription factor 8; homeobox domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=98.46  E-value=1.1e-07  Score=62.35  Aligned_cols=40  Identities=25%  Similarity=0.495  Sum_probs=37.4

Q ss_pred             ccchhhHhhhhhhhcccCCCChHHHHHHHHHhCcchhhhc
Q psy17504        156 SFKHHQLRTMKSYFNINQNPDAKDLKQLAQKTGLSKRVLQ  195 (196)
Q Consensus       156 ~ft~~Ql~~L~~~F~~~~~p~~~~r~~La~~lgL~~~~Vq  195 (196)
                      .++..|+..|+..|..++||+...|++||..+||++++||
T Consensus         9 ~p~~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~L~e~qVq   48 (64)
T 2e19_A            9 PPLKNLLSLLKAYYALNAQPSAEELSKIADSVNLPLDVVK   48 (64)
T ss_dssp             CCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHTCCHHHHH
T ss_pred             CccHHHHHHHHHHHhcCCCcCHHHHHHHHHHhCcChhhcC
Confidence            3457899999999999999999999999999999999997

>1rut_X Flinc4, fusion protein of LMO4 protein and LIM domain- binding protein 1; B-tandem zipper, protein binding; 1.30A {Mus musculus} SCOP: g.39.1.3 g.39.1.3 g.39.1.3 g.39.1.3 PDB: 2dfy_X 2xjz_I 2xjy_B

Probab=98.45  E-value=6.1e-09  Score=82.09  Aligned_cols=48  Identities=31%  Similarity=0.528  Sum_probs=42.9

Q ss_pred             HHHHHhHHHhhhhhhhhhhcceecc-CCccccccceeeeccchhhhhhc
Q psy17504          9 VMRARDLVFHLHCFTCISCGILLTK-GDLFGMRDEMIYCRPHYEILRHR   56 (196)
Q Consensus         9 v~~a~~~~~H~~CF~C~~C~~~L~~-G~~f~~~~~~~~C~~~y~~~~~~   56 (196)
                      ++.|.++.||..||+|..|+++|.. |..|+.+++++||+.||..++..
T Consensus        20 ~~~a~~~~wH~~CF~C~~C~~~L~~~g~~~~~~~g~~yC~~cy~~~~~~   68 (188)
T 1rut_X           20 LLYAMDSYWHSRCLKCSSCQAQLGDIGTSSYTKSGMILCRNDYIRLFGN   68 (188)
T ss_dssp             EEEETTEEECGGGCBCTTTCCBHHHHCSEEEEETTEEECHHHHHHHHSC
T ss_pred             eEEecCcEecccCcccCCCCcccccCCceEEEeCCcccccccccccccc
Confidence            4567899999999999999999965 67888899999999999998865

>1ic8_A Hepatocyte nuclear factor 1-alpha; transcription regulation, DNA-binding, POU domain, diabetes, disease mutation, MODY3, transcription/DNA comple; 2.60A {Homo sapiens} SCOP: a.4.1.1 a.35.1.1

Probab=98.44  E-value=3.2e-08  Score=78.60  Aligned_cols=50  Identities=12%  Similarity=0.266  Sum_probs=43.3

Q ss_pred             ccccchhhcccchhhHhhhhhhhcccCCCChHHHHHHHHHhC---------------------cchhhhcC
Q psy17504        147 HQRTKRMRTSFKHHQLRTMKSYFNINQNPDAKDLKQLAQKTG---------------------LSKRVLQN  196 (196)
Q Consensus       147 ~~k~rR~RT~ft~~Ql~~L~~~F~~~~~p~~~~r~~La~~lg---------------------L~~~~Vq~  196 (196)
                      .++.||.||.|+..|+..|+..|+.++||+...|++||..++                     |++.+|++
T Consensus       112 ~~k~rr~R~~ft~~ql~~Le~~F~~~~yp~~~~Re~la~~~~~~~~~~~G~~~~~~~glg~~~lte~~V~~  182 (194)
T 1ic8_A          112 TKKGRRNRFKWGPASQQILFQAYERQKNPSKEERETLVEECNRAECIQRGVSPSQAQGLGSNLVTEVRVYN  182 (194)
T ss_dssp             -----CCCCCCCHHHHHHHHHHHHHHCCCCTTTTHHHHHHHHHHHHHHSSCCCTTCCTTGGGCCCHHHHHH
T ss_pred             cccCCCCCcccCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCchhhccccccccccccccccccCccccch
Confidence            457788999999999999999999999999999999999999                     99999873

>2h8r_A Hepatocyte nuclear factor 1-beta; trasncription factor, POU, homeo, protein-DNA, human disease; 3.20A {Homo sapiens}

Probab=98.44  E-value=5.7e-08  Score=78.30  Aligned_cols=43  Identities=12%  Similarity=0.320  Sum_probs=38.0

Q ss_pred             cccccchhhcccchhhHhhhhhhhcccCCCChHHHHHHHHHhC
Q psy17504        146 SHQRTKRMRTSFKHHQLRTMKSYFNINQNPDAKDLKQLAQKTG  188 (196)
Q Consensus       146 ~~~k~rR~RT~ft~~Ql~~L~~~F~~~~~p~~~~r~~La~~lg  188 (196)
                      ..++.||.||.|+..|+..|+..|+.++||+...|++||..++
T Consensus       138 ~~~k~RR~R~~ft~~ql~~Le~~F~~~~YP~~~~ReeLA~~~n  180 (221)
T 2h8r_A          138 TNKKMRRNRFKWGPASQQILYQAYDRQKNPSKEEREALVEECN  180 (221)
T ss_dssp             ----CCCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHH
T ss_pred             ccCCCCCCCcCCCHHHHHHHHHHHHcCCCCCHHHHHHHHHHHC
Confidence            4567889999999999999999999999999999999999988

>1b8t_A Protein (CRP1); LIM domain, muscle differentiation, contractIle; NMR {Gallus gallus} SCOP: g.39.1.3 g.39.1.3 g.39.1.3 g.39.1.3 PDB: 1ibi_A 1qli_A 1cxx_A 1ctl_A 2o13_A

Probab=98.43  E-value=5.2e-09  Score=82.70  Aligned_cols=50  Identities=28%  Similarity=0.527  Sum_probs=42.1

Q ss_pred             hHHHHHHHHhHHHhhhhhhhhhhcceeccCCccccccceeeeccchhhhhhc
Q psy17504          5 SSELVMRARDLVFHLHCFTCISCGILLTKGDLFGMRDEMIYCRPHYEILRHR   56 (196)
Q Consensus         5 ~~~~v~~a~~~~~H~~CF~C~~C~~~L~~G~~f~~~~~~~~C~~~y~~~~~~   56 (196)
                      +.++| .+.++.||..||+|..|+++|.. ..|+.+++++||+.||..++..
T Consensus       127 ~~~~v-~a~~~~~H~~CF~C~~C~~~L~~-~~~~~~~g~~yC~~cy~~~f~~  176 (192)
T 1b8t_A          127 AAEKV-IGAGKSWHKSCFRCAKCGKSLES-TTLADKDGEIYCKGCYAKNFGP  176 (192)
T ss_dssp             SSSCE-EETTEEECTTTCBCTTTCCBCCS-SSEEEETTEEEEHHHHHHHTCC
T ss_pred             CcEEE-ecCCCccchhcCCccccCCCCCC-CcccccCCEEeCHHHHHHhcCC
Confidence            34444 48899999999999999999954 4678899999999999998864

>2l9r_A Homeobox protein NKX-3.1; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative; NMR {Homo sapiens}

Probab=98.40  E-value=1.6e-07  Score=62.47  Aligned_cols=41  Identities=17%  Similarity=0.284  Sum_probs=39.0

Q ss_pred             cccchhhHhhhhhhhcccCCCChHHHHHHHHHhCcchhhhc
Q psy17504        155 TSFKHHQLRTMKSYFNINQNPDAKDLKQLAQKTGLSKRVLQ  195 (196)
Q Consensus       155 T~ft~~Ql~~L~~~F~~~~~p~~~~r~~La~~lgL~~~~Vq  195 (196)
                      ..+|..|+.+|+..|..++||+...|++||..+||++++||
T Consensus         9 ~~~t~~ql~~LE~~F~~~~yp~~~~r~~LA~~l~Lte~qVq   49 (69)
T 2l9r_A            9 SHMSHTQVIELERKFSHQKYLSAPERAHLAKNLKLTETQVK   49 (69)
T ss_dssp             CCCCHHHHHHHHHHHHHCSCCCHHHHHHHHHHTTCCHHHHH
T ss_pred             CcCCHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCChhhee
Confidence            36789999999999999999999999999999999999997

>1b8t_A Protein (CRP1); LIM domain, muscle differentiation, contractIle; NMR {Gallus gallus} SCOP: g.39.1.3 g.39.1.3 g.39.1.3 g.39.1.3 PDB: 1ibi_A 1qli_A 1cxx_A 1ctl_A 2o13_A

Probab=98.29  E-value=6.9e-08  Score=76.19  Aligned_cols=46  Identities=24%  Similarity=0.564  Sum_probs=40.6

Q ss_pred             HHHHhHHHhhhhhhhhhhcceeccCCccccccceeeeccchhhhhhc
Q psy17504         10 MRARDLVFHLHCFTCISCGILLTKGDLFGMRDEMIYCRPHYEILRHR   56 (196)
Q Consensus        10 ~~a~~~~~H~~CF~C~~C~~~L~~G~~f~~~~~~~~C~~~y~~~~~~   56 (196)
                      +.|.++.||..||+|..|+++|. +..|+.+++++||+.||..++..
T Consensus        23 v~a~g~~wH~~CF~C~~C~~~L~-~~~~~~~~g~~yC~~cy~~~f~~   68 (192)
T 1b8t_A           23 VQCEGSSFHKSCFLCMVCKKNLD-STTVAVHGDEIYCKSCYGKKYGP   68 (192)
T ss_dssp             EEETTEEECTTTCBCTTTCCBCC-SSSEEEETTEEEEHHHHHHHHSC
T ss_pred             EEeCCceecCCCCcCcccCCcCC-CCeeEecCCEeeChhhhHhhcCc
Confidence            35889999999999999999995 44688889999999999999864

>1x2m_A LAG1 longevity assurance homolog 6; homeobox domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: a.4.1.1

Probab=98.25  E-value=6.1e-07  Score=58.74  Aligned_cols=37  Identities=24%  Similarity=0.420  Sum_probs=34.2

Q ss_pred             hhhHhhhhhhh-cccCCCChHHHHHHHHHhCcchhhhc
Q psy17504        159 HHQLRTMKSYF-NINQNPDAKDLKQLAQKTGLSKRVLQ  195 (196)
Q Consensus       159 ~~Ql~~L~~~F-~~~~~p~~~~r~~La~~lgL~~~~Vq  195 (196)
                      ..|+.+||..| ..++||+...|++||..+||+++|||
T Consensus         9 ~~~~~~LE~~F~~~~~yp~~~~r~~LA~~l~LterQVk   46 (64)
T 1x2m_A            9 AQPNAILEKVFTAITKHPDEKRLEGLSKQLDWDVRSIQ   46 (64)
T ss_dssp             SCHHHHHHHHHHTTCSSCCHHHHHHHHHHHCSCHHHHH
T ss_pred             chHHHHHHHHHHHcCCCcCHHHHHHHHHHhCCCHHHHH
Confidence            34799999999 67999999999999999999999997

>2rgt_A Fusion of LIM/homeobox protein LHX3, linker, INSU enhancer protein ISL-1; protein-protein complex, LIM domain, Zn finger, activator, D binding; 2.05A {Mus musculus} PDB: 3mmk_A

Probab=98.25  E-value=3.8e-08  Score=76.20  Aligned_cols=46  Identities=26%  Similarity=0.606  Sum_probs=39.3

Q ss_pred             HHHHHhHHHhhhhhhhhhhcceeccCCccccccceeeeccchhhhhhc
Q psy17504          9 VMRARDLVFHLHCFTCISCGILLTKGDLFGMRDEMIYCRPHYEILRHR   56 (196)
Q Consensus         9 v~~a~~~~~H~~CF~C~~C~~~L~~G~~f~~~~~~~~C~~~y~~~~~~   56 (196)
                      ++.|.++.||..||+|..|+++|. +..| .++|++||+.||..++..
T Consensus        21 ~~~a~~~~wH~~CF~C~~C~~~L~-~~~f-~~~g~~yC~~~y~~~f~~   66 (169)
T 2rgt_A           21 ILKALDRHWHSKCLKCSDCHVPLA-ERCF-SRGESVYCKDDFFKRFGT   66 (169)
T ss_dssp             CEECSSCEECTTTSBCTTTCCBCC-SCCE-ESSSCEECHHHHHHHHSC
T ss_pred             EEEECCcEEccccCccCCCCCcCC-CCCc-ccCCeeeecccccccccc
Confidence            456789999999999999999994 4445 689999999999998853

>2jtn_A LIM domain-binding protein 1, LIM/homeobox protein LHX3; intramolecular (fusion) protein-protein complex, protein binding/transcription complex; NMR {Mus musculus}

Probab=98.24  E-value=4e-08  Score=76.97  Aligned_cols=46  Identities=26%  Similarity=0.606  Sum_probs=39.0

Q ss_pred             HHHHHhHHHhhhhhhhhhhcceeccCCccccccceeeeccchhhhhhc
Q psy17504          9 VMRARDLVFHLHCFTCISCGILLTKGDLFGMRDEMIYCRPHYEILRHR   56 (196)
Q Consensus         9 v~~a~~~~~H~~CF~C~~C~~~L~~G~~f~~~~~~~~C~~~y~~~~~~   56 (196)
                      ++.|.++.||..||+|..|+++|. +..| .+++++||+.||..++..
T Consensus        75 ~~~a~~~~wH~~CF~C~~C~~~L~-~~~f-~~~g~~yC~~~y~~~f~~  120 (182)
T 2jtn_A           75 ILKALDRHWHSKCLKCSDCHVPLA-ERCF-SRGESVYCKDDFFKRFGT  120 (182)
T ss_dssp             EEEETTEEECSSTTSCTTTCCCCS-SCCE-EETTEEECHHHHHHTTSC
T ss_pred             eEEecCCeEccccCccCCCCCccC-CCce-eECCEeeecCcccccccc
Confidence            456789999999999999999994 4445 689999999999998753

>3k2a_A Homeobox protein MEIS2; homeobox domain, DNA-binding, transcription, nucleus, phosphoprotein, DNA bindi protein; 1.95A {Homo sapiens} SCOP: a.4.1.1

Probab=98.16  E-value=1e-06  Score=58.10  Aligned_cols=41  Identities=29%  Similarity=0.409  Sum_probs=37.5

Q ss_pred             ccchhhHhhhhhhhc---ccCCCChHHHHHHHHHhCcchhhhcC
Q psy17504        156 SFKHHQLRTMKSYFN---INQNPDAKDLKQLAQKTGLSKRVLQN  196 (196)
Q Consensus       156 ~ft~~Ql~~L~~~F~---~~~~p~~~~r~~La~~lgL~~~~Vq~  196 (196)
                      .|+..|+..|+..|.   .++||+..++++||..+||++.+|++
T Consensus         4 ~f~~~~~~~L~~~f~~h~~~pyp~~~~r~~La~~~~l~~~qV~~   47 (67)
T 3k2a_A            4 IFPKVATNIMRAWLFQHLTHPYPSEEQKKQLAQDTGLTILQVNN   47 (67)
T ss_dssp             --CHHHHHHHHHHHHHTTTSCCCCHHHHHHHHHHHTCCHHHHHH
T ss_pred             cCCHHHHHHHHHHHHHhccCCCCCHHHHHHHHHHhCcCHHHhhh
Confidence            689999999999999   99999999999999999999999973

>2da7_A Zinc finger homeobox protein 1B; homeobox domain, three helices with the DNA binding helix- turn-helix motif, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=98.14  E-value=1.3e-06  Score=57.85  Aligned_cols=37  Identities=19%  Similarity=0.596  Sum_probs=35.1

Q ss_pred             hhhHhhhhhhhcccCCCChHHHHHHHHHhCcchhhhc
Q psy17504        159 HHQLRTMKSYFNINQNPDAKDLKQLAQKTGLSKRVLQ  195 (196)
Q Consensus       159 ~~Ql~~L~~~F~~~~~p~~~~r~~La~~lgL~~~~Vq  195 (196)
                      .+|+..|+.+|+.|++|+..++..||..+||++++||
T Consensus        14 k~ql~~Lk~yF~~n~~Ps~eei~~LA~~lgL~~~VVr   50 (71)
T 2da7_A           14 KDHMSVLKAYYAMNMEPNSDELLKISIAVGLPQEFVK   50 (71)
T ss_dssp             THHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHH
T ss_pred             HHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCHHHHH
Confidence            4589999999999999999999999999999999997

>1mh3_A Maltose binding-A1 homeodomain protein chimera; MATA1, binding cooperativity, maltose binding protein, MBP, sugar binding, DNA binding protein; 2.10A {Escherichia coli} SCOP: a.4.1.1 c.94.1.1 PDB: 1mh4_A 1le8_A

Probab=97.84  E-value=7.6e-06  Score=70.51  Aligned_cols=48  Identities=13%  Similarity=0.221  Sum_probs=44.7

Q ss_pred             ccchhhcccchhhHhhhhhhhcccCCCChHHHHHHHHHhCcchhhhcC
Q psy17504        149 RTKRMRTSFKHHQLRTMKSYFNINQNPDAKDLKQLAQKTGLSKRVLQN  196 (196)
Q Consensus       149 k~rR~RT~ft~~Ql~~L~~~F~~~~~p~~~~r~~La~~lgL~~~~Vq~  196 (196)
                      ..++.|+.|+..|+..|++.|+.++||+..+|++||.++||+++|||+
T Consensus       364 ~~~~~~~~~~~~q~~~Le~~f~~~~yp~~~~~~~la~~~~l~~~qv~~  411 (421)
T 1mh3_A          364 AQTAAAAAISPQARAFLEQVFRRKQSLNSKEKEEVAKKCGITPLQVRV  411 (421)
T ss_dssp             HHHHHHCSSCHHHHHHHHHHHHHCSCCCHHHHHHHHHHHTSCHHHHHH
T ss_pred             hhhhhhhhhcchHHHHHHHHHhcCCCcCHHHHHHHHHHHCcCHHHhhH
Confidence            346788999999999999999999999999999999999999999973

>2lk2_A Homeobox protein TGIF1; NESG, structural genomics, northeast structural genomics CON PSI-biology, transcription; NMR {Homo sapiens}

Probab=97.53  E-value=3.3e-05  Score=53.62  Aligned_cols=41  Identities=20%  Similarity=0.314  Sum_probs=37.4

Q ss_pred             ccchhhHhhhhhhhcc---cCCCChHHHHHHHHHhCcchhhhcC
Q psy17504        156 SFKHHQLRTMKSYFNI---NQNPDAKDLKQLAQKTGLSKRVLQN  196 (196)
Q Consensus       156 ~ft~~Ql~~L~~~F~~---~~~p~~~~r~~La~~lgL~~~~Vq~  196 (196)
                      .|+..+...|+..|..   ++||+..+|++||..+||++.||++
T Consensus        11 ~l~~~~~~iL~~W~~~h~~npYPs~~ek~~LA~~tgLt~~QV~~   54 (89)
T 2lk2_A           11 MLPKESVQILRDWLYEHRYNAYPSEQEKALLSQQTHLSTLQVCN   54 (89)
T ss_dssp             CCCHHHHHHHHHHHHHTSGGGSCCHHHHHHHHHHSSSCHHHHHH
T ss_pred             cCCHHHHHHHHHHHHHhccCCCCCHHHHHHHHHHHCcCHHHHHH
Confidence            4778889999999877   9999999999999999999999974

>1j2o_A FLIN2, fusion of rhombotin-2 and LIM domain-binding protein 1; LIM-interaction-domain (LID), metal binding protein; NMR {Mus musculus} SCOP: g.39.1.3 g.39.1.3

Probab=93.11  E-value=0.023  Score=40.45  Aligned_cols=41  Identities=17%  Similarity=0.027  Sum_probs=31.1

Q ss_pred             HHHhhhhhhhh-----hhcceeccCCccccccceeeeccchhhhhh
Q psy17504         15 LVFHLHCFTCI-----SCGILLTKGDLFGMRDEMIYCRPHYEILRH   55 (196)
Q Consensus        15 ~~~H~~CF~C~-----~C~~~L~~G~~f~~~~~~~~C~~~y~~~~~   55 (196)
                      ..|...|+.|.     +|..++..|+.|.++++++||..||.....
T Consensus        62 ~~f~~~c~~c~~~~~~~~~~~~~~g~~f~~~~~~~~C~~~~~~~~~  107 (114)
T 1j2o_A           62 RLGGSGGHMGSGGDVMVVGEPTLMGGEFGDEDERLITRLENTQFDA  107 (114)
T ss_dssp             HHHTSCCSSCBSCSCCCSSCSSTTSSBCCCSSSCCCEEEECTTCCC
T ss_pred             HHhCcccCcCCCCceeEcCCccCCCCeeEEcCCEeecchhhhcccc
Confidence            44556665543     366777789999999999999999987654

>1m3v_A FLIN4, fusion of the LIM interacting domain of LDB1 and the N-terminal LIM domain of LMO4...; fusion protein, LMO proteins, metal binding protein; NMR {Mus musculus} SCOP: g.39.1.3 g.39.1.3

Probab=92.67  E-value=0.024  Score=40.80  Aligned_cols=24  Identities=25%  Similarity=0.299  Sum_probs=20.6

Q ss_pred             cCCccccccceeeeccchhhhhhc
Q psy17504         33 KGDLFGMRDEMIYCRPHYEILRHR   56 (196)
Q Consensus        33 ~G~~f~~~~~~~~C~~~y~~~~~~   56 (196)
                      .|+.|+++++++||+.||.+++..
T Consensus        93 ~g~~f~~~~~~~yC~~~~~~~~~~  116 (122)
T 1m3v_A           93 MGGEFGDEDERLITRLENTQFDAA  116 (122)
T ss_dssp             CSCTTCCTTCCCCEECTTTTTTCC
T ss_pred             CCCccEecCCEeEccCcchhchhh
Confidence            588899999999999999887643

>1zfo_A LAsp-1; LIM domain, zinc-finger, metal-binding protein; NMR {Sus scrofa} SCOP: g.39.1.4

Probab=81.44  E-value=0.055  Score=29.63  Aligned_cols=19  Identities=32%  Similarity=0.562  Sum_probs=13.5

Q ss_pred             CChHHHHHHHHhHHHhhhhh
Q psy17504          3 ISSSELVMRARDLVFHLHCF   22 (196)
Q Consensus         3 i~~~~~v~~a~~~~~H~~CF   22 (196)
                      +.+.|.++ +.++.||..||
T Consensus        13 Vy~~Ek~~-~~g~~~Hk~CF   31 (31)
T 1zfo_A           13 VYPTEKVN-CLDKFWHKACF   31 (31)
T ss_dssp             CCGGGCCC-SSSSCCCGGGC
T ss_pred             EecceeEE-ECCeEecccCC
Confidence            44455444 67899999998

---

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

Original result of RPS-BLAST against SCOP70(version1.75) database

ID	Length	Definition	E-value
Query	196
d1pufa_	77	a.4.1.1 (A:) Homeobox protein hox-a9 {Mouse (Mus m	5e-10
d1wh7a_	80	a.4.1.1 (A:) ZF-HD homeobox protein At4g24660 {Tha	1e-09
d1bw5a_	66	a.4.1.1 (A:) Insulin gene enhancer protein isl-1 {	1e-09
d1rutx3	31	g.39.1.3 (X:83-113) LIM only 4 (Lmo4) {Mouse (Mus	1e-08
d2cuea1	68	a.4.1.1 (A:7-74) Paired box protein pax6 {Human (H	3e-08
d1fjla_	65	a.4.1.1 (A:) Paired protein {Fruit fly (Drosophila	4e-08
d1yz8p1	60	a.4.1.1 (P:1-60) Pituitary homeobox 2 {Human (Homo	5e-08
d1p7ia_	53	a.4.1.1 (A:) Engrailed Homeodomain {Drosophila mel	8e-08
d1s7ea1	50	a.4.1.1 (A:103-152) Hepatocyte nuclear factor 6 {M	2e-07
d1x2na1	62	a.4.1.1 (A:6-67) Homeobox protein pknox1 {Human (H	3e-07
d1jgga_	57	a.4.1.1 (A:) Even-skipped homeodomain {Fruit fly (	4e-07
d1au7a1	58	a.4.1.1 (A:103-160) Pit-1 POU homeodomain {Rat (Ra	5e-07
d1b72a_	88	a.4.1.1 (A:) Homeobox protein hox-b1 {Human (Homo	5e-07
d2e1oa1	57	a.4.1.1 (A:8-64) Homeobox protein prh {Human (Homo	5e-07
d1ftta_	68	a.4.1.1 (A:) Thyroid transcription factor 1 homeod	8e-07
d2craa1	58	a.4.1.1 (A:7-64) Homeobox protein hox-b13 {Human (	9e-07
d9anta_	56	a.4.1.1 (A:) Antennapedia Homeodomain {Drosophila	1e-06
d1vnda_	77	a.4.1.1 (A:) VND/NK-2 protein {Fruit fly (Drosophi	2e-06
d1e3oc1	57	a.4.1.1 (C:104-160) Oct-1 POU Homeodomain {Human (	3e-06
d1ocpa_	67	a.4.1.1 (A:) Oct-3 POU Homeodomain {Mouse (Mus mus	4e-06
d1pufb_	73	a.4.1.1 (B:) pbx1 {Human (Homo sapiens) [TaxId: 96	6e-06
d1ig7a_	58	a.4.1.1 (A:) Msx-1 homeodomain {Mouse (Mus musculu	6e-06
d1zq3p1	67	a.4.1.1 (P:2-68) Homeotic bicoid protein {Fruit fl	7e-06
d1wi3a_	71	a.4.1.1 (A:) DNA-binding protein SATB2 {Human (Hom	8e-06
d1le8a_	53	a.4.1.1 (A:) Mating type protein A1 Homeodomain {B	9e-06
d2cufa1	82	a.4.1.1 (A:8-89) Homeobox-containing protein 1, HM	2e-05
d1k61a_	60	a.4.1.1 (A:) mat alpha2 Homeodomain {Baker's yeast	3e-05
d2cqxa1	59	a.4.1.1 (A:8-66) LAG1 longevity assurance homolog	1e-04
d1uhsa_	72	a.4.1.1 (A:) Homeodomain-only protein, Hop {Mouse	4e-04
d1lfba_	78	a.4.1.1 (A:) Hepatocyte nuclear factor 1a (LFB1/HN	7e-04
d1x2ma1	52	a.4.1.1 (A:8-59) Lag1 longevity assurance homolog	0.002
d1g47a2	35	g.39.1.3 (A:36-70) Pinch (particularly interesting	0.004

>d1pufa_ a.4.1.1 (A:) Homeobox protein hox-a9 {Mouse (Mus musculus) [TaxId: 10090]} Length = 77

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Homeobox protein hox-a9
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 51.8 bits (124), Expect = 5e-10
 Identities = 10/59 (16%), Positives = 26/59 (44%)

Query: 138 SSPGSGVHSHQRTKRMRTSFKHHQLRTMKSYFNINQNPDAKDLKQLAQKTGLSKRVLQN 196
           ++P +     + T++ R  +  HQ   ++  F  N         ++A+   L++R ++ 
Sbjct: 1   NNPAANWLHARSTRKKRCPYTKHQTLELEKEFLFNMYLTRDRRYEVARLLNLTERQVKI 59

>d1wh7a_ a.4.1.1 (A:) ZF-HD homeobox protein At4g24660 {Thale cress (Arabidopsis thaliana) [TaxId: 3702]} Length = 80

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: ZF-HD homeobox protein At4g24660
species: Thale cress (Arabidopsis thaliana) [TaxId: 3702]

 Score = 50.8 bits (121), Expect = 1e-09
 Identities = 19/67 (28%), Positives = 30/67 (44%), Gaps = 4/67 (5%)

Query: 134 GAGNSSPGSGVHSHQRTKRMRTSFKHHQLRTMKSYFN----INQNPDAKDLKQLAQKTGL 189
           G+  SS  +   S   TKR RT F   Q   M ++        Q  D   ++Q   +TG+
Sbjct: 1   GSSGSSGSNPSSSGGTTKRFRTKFTAEQKEKMLAFAERLGWRIQKHDDVAVEQFCAETGV 60

Query: 190 SKRVLQN 196
            ++VL+ 
Sbjct: 61  RRQVLKI 67

>d1bw5a_ a.4.1.1 (A:) Insulin gene enhancer protein isl-1 {Rat (Rattus norvegicus) [TaxId: 10116]} Length = 66

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Insulin gene enhancer protein isl-1
species: Rat (Rattus norvegicus) [TaxId: 10116]

 Score = 50.2 bits (120), Expect = 1e-09
 Identities = 19/48 (39%), Positives = 29/48 (60%)

Query: 149 RTKRMRTSFKHHQLRTMKSYFNINQNPDAKDLKQLAQKTGLSKRVLQN 196
           +T R+RT     QL T+++ +  N  PDA   +QL + TGLS RV++ 
Sbjct: 2   KTTRVRTVLNEKQLHTLRTCYAANPRPDALMKEQLVEMTGLSPRVIRV 49

>d1rutx3 g.39.1.3 (X:83-113) LIM only 4 (Lmo4) {Mouse (Mus musculus) [TaxId: 10090]} Length = 31

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: LIM only 4 (Lmo4)
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 46.6 bits (111), Expect = 1e-08
 Identities = 13/21 (61%), Positives = 16/21 (76%)

Query: 2  GISSSELVMRARDLVFHLHCF 22
           I +SELVMRA+  V+HL CF
Sbjct: 11 SIPASELVMRAQGNVYHLKCF 31

>d2cuea1 a.4.1.1 (A:7-74) Paired box protein pax6 {Human (Homo sapiens) [TaxId: 9606]} Length = 68

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Paired box protein pax6
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 46.7 bits (111), Expect = 3e-08
 Identities = 14/46 (30%), Positives = 22/46 (47%)

Query: 151 KRMRTSFKHHQLRTMKSYFNINQNPDAKDLKQLAQKTGLSKRVLQN 196
           +R RTSF   Q+  ++  F     PD    ++LA K  L +  +Q 
Sbjct: 2   QRNRTSFTQEQIEALEKEFERTHYPDVFARERLAAKIDLPEARIQV 47

>d1fjla_ a.4.1.1 (A:) Paired protein {Fruit fly (Drosophila melanogaster) [TaxId: 7227]} Length = 65

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Paired protein
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

 Score = 46.4 bits (110), Expect = 4e-08
 Identities = 16/48 (33%), Positives = 27/48 (56%)

Query: 149 RTKRMRTSFKHHQLRTMKSYFNINQNPDAKDLKQLAQKTGLSKRVLQN 196
           + +R RT+F   QL  ++  F   Q PD    ++LAQ+T L++  +Q 
Sbjct: 1   KQRRSRTTFSASQLDELERAFERTQYPDIYTREELAQRTNLTEARIQV 48

>d1yz8p1 a.4.1.1 (P:1-60) Pituitary homeobox 2 {Human (Homo sapiens) [TaxId: 9606]} Length = 60

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Pituitary homeobox 2
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 45.7 bits (108), Expect = 5e-08
 Identities = 13/46 (28%), Positives = 26/46 (56%)

Query: 151 KRMRTSFKHHQLRTMKSYFNINQNPDAKDLKQLAQKTGLSKRVLQN 196
           +R RT F   QL+ +++ F  N+ PD    +++A  T L++  ++ 
Sbjct: 2   RRQRTHFTSQQLQQLEATFQRNRYPDMSTREEIAVWTNLTEARVRV 47

>d1p7ia_ a.4.1.1 (A:) Engrailed Homeodomain {Drosophila melanogaster [TaxId: 7227]} Length = 53

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Engrailed Homeodomain
species: Drosophila melanogaster [TaxId: 7227]

 Score = 45.2 bits (107), Expect = 8e-08
 Identities = 14/45 (31%), Positives = 25/45 (55%)

Query: 152 RMRTSFKHHQLRTMKSYFNINQNPDAKDLKQLAQKTGLSKRVLQN 196
           R RT+F   QL  +K  FN N+    +  +QL+ + GL++  ++ 
Sbjct: 1   RPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKI 45

>d1s7ea1 a.4.1.1 (A:103-152) Hepatocyte nuclear factor 6 {Mouse (Mus musculus) [TaxId: 10090]} Length = 50

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Hepatocyte nuclear factor 6
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 44.1 bits (104), Expect = 2e-07
 Identities = 12/43 (27%), Positives = 20/43 (46%)

Query: 154 RTSFKHHQLRTMKSYFNINQNPDAKDLKQLAQKTGLSKRVLQN 196
           R  F   Q RT+ + F  N+ P  +    ++Q+ GL    + N
Sbjct: 2   RLVFTDVQRRTLHAIFKENKRPSKELQITISQQLGLELSTVSN 44

>d1x2na1 a.4.1.1 (A:6-67) Homeobox protein pknox1 {Human (Homo sapiens) [TaxId: 9606]} Length = 62

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Homeobox protein pknox1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 43.6 bits (103), Expect = 3e-07
 Identities = 12/49 (24%), Positives = 20/49 (40%), Gaps = 3/49 (6%)

Query: 151 KRMRTSFKHHQLRTMKSYFNINQN---PDAKDLKQLAQKTGLSKRVLQN 196
           K  R     H    M+S+   +     P   + KQ+A +T L+   + N
Sbjct: 3   KNKRGVLPKHATNVMRSWLFQHIGHPYPTEDEKKQIAAQTNLTLLQVNN 51

>d1jgga_ a.4.1.1 (A:) Even-skipped homeodomain {Fruit fly (Drosophila melanogaster) [TaxId: 7227]} Length = 57

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Even-skipped homeodomain
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

 Score = 43.4 bits (102), Expect = 4e-07
 Identities = 10/45 (22%), Positives = 18/45 (40%)

Query: 152 RMRTSFKHHQLRTMKSYFNINQNPDAKDLKQLAQKTGLSKRVLQN 196
           R RT+F   QL  ++  F            +LA +  L +  ++ 
Sbjct: 1   RYRTAFTRDQLGRLEKEFYKENYVSRPRRCELAAQLNLPESTIKV 45

>d1au7a1 a.4.1.1 (A:103-160) Pit-1 POU homeodomain {Rat (Rattus norvegicus) [TaxId: 10116]} Length = 58

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Pit-1 POU homeodomain
species: Rat (Rattus norvegicus) [TaxId: 10116]

 Score = 43.4 bits (102), Expect = 5e-07
 Identities = 8/45 (17%), Positives = 24/45 (53%)

Query: 152 RMRTSFKHHQLRTMKSYFNINQNPDAKDLKQLAQKTGLSKRVLQN 196
           + RT+        ++ +F  +  P ++++ ++A++  L K V++ 
Sbjct: 1   KRRTTISIAAKDALERHFGEHSKPSSQEIMRMAEELNLEKEVVRV 45

>d1b72a_ a.4.1.1 (A:) Homeobox protein hox-b1 {Human (Homo sapiens) [TaxId: 9606]} Length = 88

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Homeobox protein hox-b1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 43.8 bits (103), Expect = 5e-07
 Identities = 9/59 (15%), Positives = 22/59 (37%)

Query: 138 SSPGSGVHSHQRTKRMRTSFKHHQLRTMKSYFNINQNPDAKDLKQLAQKTGLSKRVLQN 196
            +             +RT+F   QL  ++  F+ N+        ++A    L++  ++ 
Sbjct: 15  KTAKVSEPGLGSPSGLRTNFTTRQLTELEKEFHFNKYLSRARRVEIAATLELNETQVKI 73

>d2e1oa1 a.4.1.1 (A:8-64) Homeobox protein prh {Human (Homo sapiens) [TaxId: 9606]} Length = 57

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Homeobox protein prh
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 42.9 bits (101), Expect = 5e-07
 Identities = 10/46 (21%), Positives = 21/46 (45%)

Query: 151 KRMRTSFKHHQLRTMKSYFNINQNPDAKDLKQLAQKTGLSKRVLQN 196
           K  +  F + Q   ++  F   +     + K+LA+   LS+R ++ 
Sbjct: 1   KGGQVRFSNDQTIELEKKFETQKYLSPPERKRLAKMLQLSERQVKT 46

>d1ftta_ a.4.1.1 (A:) Thyroid transcription factor 1 homeodomain {Rat (Rattus norvegicus) [TaxId: 10116]} Length = 68

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Thyroid transcription factor 1 homeodomain
species: Rat (Rattus norvegicus) [TaxId: 10116]

 Score = 42.6 bits (100), Expect = 8e-07
 Identities = 8/46 (17%), Positives = 19/46 (41%)

Query: 151 KRMRTSFKHHQLRTMKSYFNINQNPDAKDLKQLAQKTGLSKRVLQN 196
           ++ R  F   Q+  ++  F   +   A + + LA    L+   ++ 
Sbjct: 3   RKRRVLFSQAQVYELERRFKQQKYLSAPEREHLASMIHLTPTQVKI 48

>d2craa1 a.4.1.1 (A:7-64) Homeobox protein hox-b13 {Human (Homo sapiens) [TaxId: 9606]} Length = 58

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Homeobox protein hox-b13
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 42.6 bits (100), Expect = 9e-07
 Identities = 9/46 (19%), Positives = 22/46 (47%)

Query: 151 KRMRTSFKHHQLRTMKSYFNINQNPDAKDLKQLAQKTGLSKRVLQN 196
           ++ R  +   QLR ++  +  N+       ++++  T LS+R +  
Sbjct: 2   RKKRIPYSKGQLRELEREYAANKFITKDKRRKISAATSLSERQITI 47

>d9anta_ a.4.1.1 (A:) Antennapedia Homeodomain {Drosophila melanogaster [TaxId: 7227]} Length = 56

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Antennapedia Homeodomain
species: Drosophila melanogaster [TaxId: 7227]

 Score = 42.1 bits (99), Expect = 1e-06
 Identities = 7/43 (16%), Positives = 21/43 (48%)

Query: 154 RTSFKHHQLRTMKSYFNINQNPDAKDLKQLAQKTGLSKRVLQN 196
           R ++  +Q   ++  F+ N+    +   ++A    L++R ++ 
Sbjct: 1   RQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKI 43

>d1vnda_ a.4.1.1 (A:) VND/NK-2 protein {Fruit fly (Drosophila melanogaster) [TaxId: 7227]} Length = 77

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: VND/NK-2 protein
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

 Score = 42.0 bits (98), Expect = 2e-06
 Identities = 8/49 (16%), Positives = 19/49 (38%)

Query: 148 QRTKRMRTSFKHHQLRTMKSYFNINQNPDAKDLKQLAQKTGLSKRVLQN 196
            + ++ R  F   Q   ++  F   +   A + + LA    L+   ++ 
Sbjct: 7   NKKRKRRVLFTKAQTYELERRFRQQRYLSAPEREHLASLIRLTPTQVKI 55

>d1e3oc1 a.4.1.1 (C:104-160) Oct-1 POU Homeodomain {Human (Homo sapiens) [TaxId: 9606]} Length = 57

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Oct-1 POU Homeodomain
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 41.1 bits (96), Expect = 3e-06
 Identities = 11/43 (25%), Positives = 24/43 (55%)

Query: 154 RTSFKHHQLRTMKSYFNINQNPDAKDLKQLAQKTGLSKRVLQN 196
           RTS + +    ++  F  NQ P ++D+  +A++  + K V++ 
Sbjct: 2   RTSIETNIRVALEKSFMENQKPTSEDITLIAEQLNMEKEVIRV 44

>d1ocpa_ a.4.1.1 (A:) Oct-3 POU Homeodomain {Mouse (Mus musculus) [TaxId: 10090]} Length = 67

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Oct-3 POU Homeodomain
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 40.8 bits (95), Expect = 4e-06
 Identities = 13/49 (26%), Positives = 25/49 (51%)

Query: 148 QRTKRMRTSFKHHQLRTMKSYFNINQNPDAKDLKQLAQKTGLSKRVLQN 196
           Q  KR RTS ++    ++++ F     P  + +  +A + GL K V++ 
Sbjct: 6   QARKRKRTSIENRVRWSLETMFLKCPKPSLQQITHIANQLGLEKDVVRV 54

>d1pufb_ a.4.1.1 (B:) pbx1 {Human (Homo sapiens) [TaxId: 9606]} Length = 73

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: pbx1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 40.7 bits (95), Expect = 6e-06
 Identities = 12/49 (24%), Positives = 22/49 (44%), Gaps = 3/49 (6%)

Query: 151 KRMRTSFKHHQLRTMKSYFN---INQNPDAKDLKQLAQKTGLSKRVLQN 196
           +R R +F       +  YF     N  P  +  ++LA+K G++   + N
Sbjct: 2   RRKRRNFNKQATEILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSN 50

>d1ig7a_ a.4.1.1 (A:) Msx-1 homeodomain {Mouse (Mus musculus) [TaxId: 10090]} Length = 58

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Msx-1 homeodomain
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 40.3 bits (94), Expect = 6e-06
 Identities = 8/46 (17%), Positives = 19/46 (41%)

Query: 151 KRMRTSFKHHQLRTMKSYFNINQNPDAKDLKQLAQKTGLSKRVLQN 196
           ++ RT F   QL  ++  F   Q     +  + +    L++  ++ 
Sbjct: 1   RKPRTPFTTAQLLALERKFRQKQYLSIAERAEFSSSLSLTETQVKI 46

>d1zq3p1 a.4.1.1 (P:2-68) Homeotic bicoid protein {Fruit fly (Drosophila melanogaster) [TaxId: 7227]} Length = 67

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Homeotic bicoid protein
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

 Score = 40.3 bits (94), Expect = 7e-06
 Identities = 11/46 (23%), Positives = 21/46 (45%)

Query: 151 KRMRTSFKHHQLRTMKSYFNINQNPDAKDLKQLAQKTGLSKRVLQN 196
           +R RT+F   Q+  ++ +F   +   A  L  L+ K  L    ++ 
Sbjct: 2   RRTRTTFTSSQIAELEQHFLQGRYLTAPRLADLSAKLALGTAQVKI 47

>d1wi3a_ a.4.1.1 (A:) DNA-binding protein SATB2 {Human (Homo sapiens) [TaxId: 9606]} Length = 71

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: DNA-binding protein SATB2
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 40.1 bits (93), Expect = 8e-06
 Identities = 11/52 (21%), Positives = 21/52 (40%), Gaps = 1/52 (1%)

Query: 146 SHQRTKRMRTSFKHHQLRTMKSYF-NINQNPDAKDLKQLAQKTGLSKRVLQN 196
           S     R RT      L  ++S+  ++   PD + +  L+ +  L K  +  
Sbjct: 3   SGSSGPRSRTKISLEALGILQSFIHDVGLYPDQEAIHTLSAQLDLPKHTIIK 54

>d1le8a_ a.4.1.1 (A:) Mating type protein A1 Homeodomain {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 53

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Mating type protein A1 Homeodomain
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 39.5 bits (92), Expect = 9e-06
 Identities = 7/43 (16%), Positives = 23/43 (53%)

Query: 154 RTSFKHHQLRTMKSYFNINQNPDAKDLKQLAQKTGLSKRVLQN 196
           ++S        ++  F   Q+ ++K+ +++A+K G++   ++ 
Sbjct: 1   KSSISPQARAFLEQVFRRKQSLNSKEKEEVAKKCGITPLQVRV 43

>d2cufa1 a.4.1.1 (A:8-89) Homeobox-containing protein 1, HMBOX1 (Flj21616) {Human (Homo sapiens) [TaxId: 9606]} Length = 82

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Homeobox-containing protein 1, HMBOX1 (Flj21616)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 39.7 bits (92), Expect = 2e-05
 Identities = 12/44 (27%), Positives = 20/44 (45%)

Query: 152 RMRTSFKHHQLRTMKSYFNINQNPDAKDLKQLAQKTGLSKRVLQ 195
             R +++   L  M+SYFN NQ PD    +++A       +   
Sbjct: 2   GSRFTWRKECLAVMESYFNENQYPDEAKREEIANACNAVIQKPG 45

>d1k61a_ a.4.1.1 (A:) mat alpha2 Homeodomain {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 60

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: mat alpha2 Homeodomain
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 38.6 bits (90), Expect = 3e-05
 Identities = 15/51 (29%), Positives = 24/51 (47%), Gaps = 7/51 (13%)

Query: 149 RTKRMRTSFKHHQLRTMKSYFNINQN---PDAKDLKQLAQKTGLSKRVLQN 196
           R  R    F    +R ++S+F  N      D K L+ L + T LS+  ++N
Sbjct: 1   RGHR----FTKENVRILESWFAKNIENPYLDTKGLENLMKNTSLSRIQIKN 47

>d2cqxa1 a.4.1.1 (A:8-66) LAG1 longevity assurance homolog 5, LASS5 {Mouse (Mus musculus) [TaxId: 10090]} Length = 59

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: LAG1 longevity assurance homolog 5, LASS5
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 36.7 bits (85), Expect = 1e-04
 Identities = 12/46 (26%), Positives = 21/46 (45%), Gaps = 1/46 (2%)

Query: 152 RMRTSFKHHQLRTMKSYFN-INQNPDAKDLKQLAQKTGLSKRVLQN 196
           +     K     T++  F  + + PD K LK L+++   S R +Q 
Sbjct: 3   KDSPVNKVEPNDTLEKVFVSVTKYPDEKRLKGLSKQLDWSVRKIQC 48

>d1uhsa_ a.4.1.1 (A:) Homeodomain-only protein, Hop {Mouse (Mus musculus) [TaxId: 10090]} Length = 72

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Homeodomain-only protein, Hop
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 35.7 bits (82), Expect = 4e-04
 Identities = 10/47 (21%), Positives = 18/47 (38%), Gaps = 1/47 (2%)

Query: 151 KRMRTSFKHHQLRTMKSYFNINQN-PDAKDLKQLAQKTGLSKRVLQN 196
                +    Q+  ++  FN     PD   L  +A + GL++   Q 
Sbjct: 2   SEGAATMTEDQVEILEYNFNKVNKHPDPTTLCLIAAEAGLTEEQTQK 48

>d1lfba_ a.4.1.1 (A:) Hepatocyte nuclear factor 1a (LFB1/HNF1) {Rat (Rattus rattus) [TaxId: 10117]} Length = 78

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Hepatocyte nuclear factor 1a (LFB1/HNF1)
species: Rat (Rattus rattus) [TaxId: 10117]

 Score = 35.1 bits (80), Expect = 7e-04
 Identities = 4/37 (10%), Positives = 15/37 (40%)

Query: 154 RTSFKHHQLRTMKSYFNINQNPDAKDLKQLAQKTGLS 190
           R  +     + +   +   +NP  ++ + L ++   +
Sbjct: 1   RFKWGPASQQILFQAYERQKNPSKEERETLVEECNRA 37

>d1x2ma1 a.4.1.1 (A:8-59) Lag1 longevity assurance homolog 6, LASS6 {Mouse (Mus musculus) [TaxId: 10090]} Length = 52

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Lag1 longevity assurance homolog 6, LASS6
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 32.8 bits (75), Expect = 0.002
 Identities = 9/38 (23%), Positives = 18/38 (47%), Gaps = 1/38 (2%)

Query: 160 HQLRTMKSYFN-INQNPDAKDLKQLAQKTGLSKRVLQN 196
                ++  F  I ++PD K L+ L+++     R +Q 
Sbjct: 3   QPNAILEKVFTAITKHPDEKRLEGLSKQLDWDVRSIQR 40

>d1g47a2 g.39.1.3 (A:36-70) Pinch (particularly interesting new Cys-His) protein {Human (Homo sapiens) [TaxId: 9606]} Length = 35

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Pinch (particularly interesting new Cys-His) protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 32.0 bits (73), Expect = 0.004
 Identities = 8/32 (25%), Positives = 12/32 (37%), Gaps = 1/32 (3%)

Query: 22 FTCISCGILLTKGDLFGMRDEMIYCRPHYEIL 53
          F C  C        LF   +   YC   +++L
Sbjct: 1  FVCAQCFQQF-PEGLFYEFEGRKYCEHDFQML 31

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	196
d1vnda_	77	VND/NK-2 protein {Fruit fly (Drosophila melanogast	99.22
d2cuea1	68	Paired box protein pax6 {Human (Homo sapiens) [Tax	99.21
d1ig7a_	58	Msx-1 homeodomain {Mouse (Mus musculus) [TaxId: 10	99.2
d1p7ia_	53	Engrailed Homeodomain {Drosophila melanogaster [Ta	99.19
d2craa1	58	Homeobox protein hox-b13 {Human (Homo sapiens) [Ta	99.19
d1pufa_	77	Homeobox protein hox-a9 {Mouse (Mus musculus) [Tax	99.18
d1wh7a_	80	ZF-HD homeobox protein At4g24660 {Thale cress (Ara	99.18
d1zq3p1	67	Homeotic bicoid protein {Fruit fly (Drosophila mel	99.16
d1fjla_	65	Paired protein {Fruit fly (Drosophila melanogaster	99.15
d1ftta_	68	Thyroid transcription factor 1 homeodomain {Rat (R	99.15
d1jgga_	57	Even-skipped homeodomain {Fruit fly (Drosophila me	99.14
d1bw5a_	66	Insulin gene enhancer protein isl-1 {Rat (Rattus n	99.11
d2e1oa1	57	Homeobox protein prh {Human (Homo sapiens) [TaxId:	99.11
d1yz8p1	60	Pituitary homeobox 2 {Human (Homo sapiens) [TaxId:	99.1
d1b72a_	88	Homeobox protein hox-b1 {Human (Homo sapiens) [Tax	99.08
d9anta_	56	Antennapedia Homeodomain {Drosophila melanogaster	99.08
d1ocpa_	67	Oct-3 POU Homeodomain {Mouse (Mus musculus) [TaxId	99.05
d1s7ea1	50	Hepatocyte nuclear factor 6 {Mouse (Mus musculus)	99.05
d1wi3a_	71	DNA-binding protein SATB2 {Human (Homo sapiens) [T	99.02
d1uhsa_	72	Homeodomain-only protein, Hop {Mouse (Mus musculus	98.95
d1au7a1	58	Pit-1 POU homeodomain {Rat (Rattus norvegicus) [Ta	98.92
d1le8a_	53	Mating type protein A1 Homeodomain {Baker's yeast	98.9
d2cufa1	82	Homeobox-containing protein 1, HMBOX1 (Flj21616) {	98.85
d1e3oc1	57	Oct-1 POU Homeodomain {Human (Homo sapiens) [TaxId	98.79
d1pufb_	73	pbx1 {Human (Homo sapiens) [TaxId: 9606]}	98.69
d2ecca1	76	Homeobox-leucine zipper protein Homez {Human (Homo	98.52
d1lfba_	78	Hepatocyte nuclear factor 1a (LFB1/HNF1) {Rat (Rat	98.51
d2ecba1	76	Zinc fingers and homeoboxes protein 1, ZHX1 {Human	98.51
d1x2na1	62	Homeobox protein pknox1 {Human (Homo sapiens) [Tax	98.44
d1g47a2	35	Pinch (particularly interesting new Cys-His) prote	98.3
d1rutx3	31	LIM only 4 (Lmo4) {Mouse (Mus musculus) [TaxId: 10	98.29
d1k61a_	60	mat alpha2 Homeodomain {Baker's yeast (Saccharomyc	98.27
d2cqxa1	59	LAG1 longevity assurance homolog 5, LASS5 {Mouse (	98.24
d1x2ma1	52	Lag1 longevity assurance homolog 6, LASS6 {Mouse (	98.19
d1rutx4	33	LIM only 4 (Lmo4) {Mouse (Mus musculus) [TaxId: 10	97.95
d1u5sb2	35	Pinch (particularly interesting new Cys-His) prote	97.77
d2d8za2	32	Four and a half LIM domains protein 2, FHL2 {Human	97.76
d2dj7a1	31	Actin-binding LIM protein 3, abLIM-3 {Human (Homo	97.71
d2d8ya2	42	Eplin, LIMA1 {Human (Homo sapiens) [TaxId: 9606]}	97.69
d1x3ha2	32	Leupaxin {Human (Homo sapiens) [TaxId: 9606]}	97.67
d2cuqa1	32	Four and a half LIM domains 3, FHL3 {Human (Homo s	97.56
d1ibia2	31	Cysteine-rich (intestinal) protein, CRP, CRIP {Jap	97.25
d1b8ta4	49	Cysteine-rich (intestinal) protein, CRP, CRIP {Chi	97.13
d2dloa2	33	Thyroid receptor interacting protein 6, TRIP6 {Hum	97.09
d1x61a2	32	Thyroid receptor interacting protein 6, TRIP6 {Hum	96.87
d2cura1	31	Four and a half LIM domains protein 1, FHL-1 {Huma	96.73
d1imla2	48	Cysteine-rich (intestinal) protein, CRP, CRIP {Rat	96.59
d1b8ta2	65	Cysteine-rich (intestinal) protein, CRP, CRIP {Chi	96.56
d1x6aa2	34	Lim domain kinase 2 {Human (Homo sapiens) [TaxId:	96.54
d2cu8a2	33	Cysteine-rich (intestinal) protein, CRP, CRIP {Hum	96.5
d1a7ia2	32	Cysteine-rich (intestinal) protein, CRP, CRIP {Jap	96.48
d2dara1	32	PDZ and LIM domain protein 5, Enigma {Human (Homo	95.98
d1rutx2	34	LIM only 4 (Lmo4) {Mouse (Mus musculus) [TaxId: 10	95.83
d1x4ka1	32	Four and a half LIM domains protein 2, FHL2 {Human	94.64
d1wyha1	32	Four and a half LIM domains 3, FHL3 {Human (Homo s	94.24
d2co8a1	33	Nedd9 interacting protein with calponin homology,	93.75
d2dloa1	35	Thyroid receptor interacting protein 6, TRIP6 {Hum	92.63
d1x64a2	31	PDZ and LIM domain protein 3, PDLIM3 {Mouse (Mus m	90.73
d1v6ga2	40	Actin-binding LIM protein 2, abLIM2 {Human (Homo s	90.36
d1x63a2	32	Four and a half LIM domains protein 1, FHL-1 {Huma	89.78
d1j2oa2	33	Rhombotin-2 (Lmo2) {Mouse (Mus musculus) [TaxId: 1	89.06
d1x3ha1	35	Leupaxin {Human (Homo sapiens) [TaxId: 9606]}	88.32
d1x62a1	31	PDZ and LIM domain protein 1 Elfin {Human (Homo sa	87.96
d2d8xa2	26	Pinch (particularly interesting new Cys-His) prote	87.35
d2dj7a2	36	Actin-binding LIM protein 3, abLIM-3 {Human (Homo	86.94
d2cupa2	31	Four and a half LIM domains protein 1, FHL-1 {Huma	85.36
d1x68a2	34	Four and a half LIM domains protein 5, FHL-5 {Huma	80.3

>d1vnda_ a.4.1.1 (A:) VND/NK-2 protein {Fruit fly (Drosophila melanogaster) [TaxId: 7227]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: VND/NK-2 protein
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

Probab=99.22  E-value=3e-12  Score=85.82  Aligned_cols=49  Identities=16%  Similarity=0.244  Sum_probs=46.0

Q ss_pred             ccccchhhcccchhhHhhhhhhhcccCCCChHHHHHHHHHhCcchhhhc
Q psy17504        147 HQRTKRMRTSFKHHQLRTMKSYFNINQNPDAKDLKQLAQKTGLSKRVLQ  195 (196)
Q Consensus       147 ~~k~rR~RT~ft~~Ql~~L~~~F~~~~~p~~~~r~~La~~lgL~~~~Vq  195 (196)
                      ..+.||.||.||.+|+.+|+..|+.++||+...+++||..+||++.+|+
T Consensus         6 p~k~rr~Rt~ft~~Q~~~Le~~F~~~~yP~~~~r~~LA~~l~l~~~qV~   54 (77)
T d1vnda_           6 PNKKRKRRVLFTKAQTYELERRFRQQRYLSAPEREHLASLIRLTPTQVK   54 (77)
T ss_dssp             SSSSCSSCCCCCTTHHHHHHHHHHHCSCCCHHHHHHHHHHHTCCHHHHH
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHhCCChhhhh
Confidence            3466778999999999999999999999999999999999999999997

>d2cuea1 a.4.1.1 (A:7-74) Paired box protein pax6 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Paired box protein pax6
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.21  E-value=3.4e-12  Score=83.56  Aligned_cols=45  Identities=31%  Similarity=0.464  Sum_probs=43.4

Q ss_pred             chhhcccchhhHhhhhhhhcccCCCChHHHHHHHHHhCcchhhhc
Q psy17504        151 KRMRTSFKHHQLRTMKSYFNINQNPDAKDLKQLAQKTGLSKRVLQ  195 (196)
Q Consensus       151 rR~RT~ft~~Ql~~L~~~F~~~~~p~~~~r~~La~~lgL~~~~Vq  195 (196)
                      ||.||+||..|+.+|+..|..++||+...|++||..+||++.+|+
T Consensus         2 rR~Rt~ft~~Ql~~Le~~F~~n~yP~~~~r~~LA~~l~L~~~~V~   46 (68)
T d2cuea1           2 QRNRTSFTQEQIEALEKEFERTHYPDVFARERLAAKIDLPEARIQ   46 (68)
T ss_dssp             CCCCCCSCHHHHHHHHHHHTTCSSCCHHHHHHHHHHTTCCHHHHH
T ss_pred             CCCCCcCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHhCcChhhee
Confidence            568999999999999999999999999999999999999999997

>d1ig7a_ a.4.1.1 (A:) Msx-1 homeodomain {Mouse (Mus musculus) [TaxId: 10090]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Msx-1 homeodomain
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.20  E-value=3.6e-12  Score=80.87  Aligned_cols=45  Identities=18%  Similarity=0.301  Sum_probs=43.2

Q ss_pred             chhhcccchhhHhhhhhhhcccCCCChHHHHHHHHHhCcchhhhc
Q psy17504        151 KRMRTSFKHHQLRTMKSYFNINQNPDAKDLKQLAQKTGLSKRVLQ  195 (196)
Q Consensus       151 rR~RT~ft~~Ql~~L~~~F~~~~~p~~~~r~~La~~lgL~~~~Vq  195 (196)
                      ||.||.||.+|+.+|+..|+.++||+...+++||..+||++.+|+
T Consensus         1 rr~Rt~ft~~Ql~~Le~~F~~~~yP~~~~r~~LA~~l~l~~~~V~   45 (58)
T d1ig7a_           1 RKPRTPFTTAQLLALERKFRQKQYLSIAERAEFSSSLSLTETQVK   45 (58)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHHCSCCCHHHHHHHHHHTTCCHHHHH
T ss_pred             CCCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHhCCChhhee
Confidence            468999999999999999999999999999999999999999996

>d1p7ia_ a.4.1.1 (A:) Engrailed Homeodomain {Drosophila melanogaster [TaxId: 7227]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Engrailed Homeodomain
species: Drosophila melanogaster [TaxId: 7227]

Probab=99.19  E-value=3.9e-12  Score=79.25  Aligned_cols=44  Identities=32%  Similarity=0.464  Sum_probs=42.6

Q ss_pred             hhhcccchhhHhhhhhhhcccCCCChHHHHHHHHHhCcchhhhc
Q psy17504        152 RMRTSFKHHQLRTMKSYFNINQNPDAKDLKQLAQKTGLSKRVLQ  195 (196)
Q Consensus       152 R~RT~ft~~Ql~~L~~~F~~~~~p~~~~r~~La~~lgL~~~~Vq  195 (196)
                      |.||.||..|+..|+..|+.++||+...|++||..+||++.+||
T Consensus         1 R~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~lgL~~~qV~   44 (53)
T d1p7ia_           1 RPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIK   44 (53)
T ss_dssp             CCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHH
T ss_pred             CCCccCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHhCCChHHhh
Confidence            57999999999999999999999999999999999999999997

>d2craa1 a.4.1.1 (A:7-64) Homeobox protein hox-b13 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Homeobox protein hox-b13
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.19  E-value=4e-12  Score=80.63  Aligned_cols=45  Identities=20%  Similarity=0.380  Sum_probs=43.3

Q ss_pred             chhhcccchhhHhhhhhhhcccCCCChHHHHHHHHHhCcchhhhc
Q psy17504        151 KRMRTSFKHHQLRTMKSYFNINQNPDAKDLKQLAQKTGLSKRVLQ  195 (196)
Q Consensus       151 rR~RT~ft~~Ql~~L~~~F~~~~~p~~~~r~~La~~lgL~~~~Vq  195 (196)
                      ||.||.||..|+.+|+..|+.++||+...+++||..+||++.+||
T Consensus         2 rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~   46 (58)
T d2craa1           2 RKKRIPYSKGQLRELEREYAANKFITKDKRRKISAATSLSERQIT   46 (58)
T ss_dssp             CCSCCCSCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTCCCHHHHH
T ss_pred             CCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCHHHee
Confidence            567999999999999999999999999999999999999999997

>d1pufa_ a.4.1.1 (A:) Homeobox protein hox-a9 {Mouse (Mus musculus) [TaxId: 10090]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Homeobox protein hox-a9
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.18  E-value=6.7e-12  Score=84.01  Aligned_cols=48  Identities=19%  Similarity=0.291  Sum_probs=45.0

Q ss_pred             cccchhhcccchhhHhhhhhhhcccCCCChHHHHHHHHHhCcchhhhc
Q psy17504        148 QRTKRMRTSFKHHQLRTMKSYFNINQNPDAKDLKQLAQKTGLSKRVLQ  195 (196)
Q Consensus       148 ~k~rR~RT~ft~~Ql~~L~~~F~~~~~p~~~~r~~La~~lgL~~~~Vq  195 (196)
                      +..||.||.||..|+.+|+..|+.++||+...|+.||..+||++.+||
T Consensus        11 ~~~rr~Rt~ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~l~l~~~qV~   58 (77)
T d1pufa_          11 RSTRKKRCPYTKHQTLELEKEFLFNMYLTRDRRYEVARLLNLTERQVK   58 (77)
T ss_dssp             CTTSCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHH
T ss_pred             CcCCCCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHhCCCHHHhh
Confidence            345678999999999999999999999999999999999999999996

>d1wh7a_ a.4.1.1 (A:) ZF-HD homeobox protein At4g24660 {Thale cress (Arabidopsis thaliana) [TaxId: 3702]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: ZF-HD homeobox protein At4g24660
species: Thale cress (Arabidopsis thaliana) [TaxId: 3702]

Probab=99.18  E-value=8.5e-12  Score=84.17  Aligned_cols=48  Identities=31%  Similarity=0.456  Sum_probs=44.0

Q ss_pred             cccchhhcccchhhHhhhhhhhcc----cCCCChHHHHHHHHHhCcchhhhc
Q psy17504        148 QRTKRMRTSFKHHQLRTMKSYFNI----NQNPDAKDLKQLAQKTGLSKRVLQ  195 (196)
Q Consensus       148 ~k~rR~RT~ft~~Ql~~L~~~F~~----~~~p~~~~r~~La~~lgL~~~~Vq  195 (196)
                      .+.||.||.||.+|++.|+..|+.    ++||+..++++||..|||++.+||
T Consensus        15 ~~~kR~Rt~ft~~Q~~~L~~~fe~~~~~~~~p~~~~~~~la~~~gl~~~~i~   66 (80)
T d1wh7a_          15 GTTKRFRTKFTAEQKEKMLAFAERLGWRIQKHDDVAVEQFCAETGVRRQVLK   66 (80)
T ss_dssp             CCSSCCCCCCCHHHHHHHHHHHHHHTSCCCSSTTHHHHHHHHHSCCCHHHHH
T ss_pred             cCCCCccccCCHHHHHHHHHHHHHhcccccCcCHHHHHHHHHHHCCCHHHee
Confidence            456789999999999999888875    899999999999999999999997

>d1zq3p1 a.4.1.1 (P:2-68) Homeotic bicoid protein {Fruit fly (Drosophila melanogaster) [TaxId: 7227]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Homeotic bicoid protein
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

Probab=99.16  E-value=8.7e-12  Score=81.33  Aligned_cols=46  Identities=24%  Similarity=0.352  Sum_probs=43.9

Q ss_pred             cchhhcccchhhHhhhhhhhcccCCCChHHHHHHHHHhCcchhhhc
Q psy17504        150 TKRMRTSFKHHQLRTMKSYFNINQNPDAKDLKQLAQKTGLSKRVLQ  195 (196)
Q Consensus       150 ~rR~RT~ft~~Ql~~L~~~F~~~~~p~~~~r~~La~~lgL~~~~Vq  195 (196)
                      +||.||.||..|+.+|+..|+.++||+...+.+||..+||++.+|+
T Consensus         1 Prr~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~~V~   46 (67)
T d1zq3p1           1 PRRTRTTFTSSQIAELEQHFLQGRYLTAPRLADLSAKLALGTAQVK   46 (67)
T ss_dssp             CSCCSCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHTSCHHHHH
T ss_pred             CCCCCCcCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHhCCCcccee
Confidence            3678999999999999999999999999999999999999999997

>d1fjla_ a.4.1.1 (A:) Paired protein {Fruit fly (Drosophila melanogaster) [TaxId: 7227]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Paired protein
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

Probab=99.15  E-value=7.6e-12  Score=81.13  Aligned_cols=47  Identities=34%  Similarity=0.519  Sum_probs=44.8

Q ss_pred             ccchhhcccchhhHhhhhhhhcccCCCChHHHHHHHHHhCcchhhhc
Q psy17504        149 RTKRMRTSFKHHQLRTMKSYFNINQNPDAKDLKQLAQKTGLSKRVLQ  195 (196)
Q Consensus       149 k~rR~RT~ft~~Ql~~L~~~F~~~~~p~~~~r~~La~~lgL~~~~Vq  195 (196)
                      |.||.||.||..|+..|+..|..++||+...+++||..+||++.+|+
T Consensus         1 k~rr~Rt~ft~~Q~~~Le~~F~~n~yPs~~~r~~LA~~lgl~~~~V~   47 (65)
T d1fjla_           1 KQRRSRTTFSASQLDELERAFERTQYPDIYTREELAQRTNLTEARIQ   47 (65)
T ss_dssp             CCCCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHH
T ss_pred             CCCCCCCCCCHHHHHHHHHHHHHcCCCChHHHHHHHHHhCCCHHHhh
Confidence            45779999999999999999999999999999999999999999996

>d1ftta_ a.4.1.1 (A:) Thyroid transcription factor 1 homeodomain {Rat (Rattus norvegicus) [TaxId: 10116]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Thyroid transcription factor 1 homeodomain
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=99.15  E-value=8.3e-12  Score=81.66  Aligned_cols=46  Identities=17%  Similarity=0.273  Sum_probs=44.0

Q ss_pred             cchhhcccchhhHhhhhhhhcccCCCChHHHHHHHHHhCcchhhhc
Q psy17504        150 TKRMRTSFKHHQLRTMKSYFNINQNPDAKDLKQLAQKTGLSKRVLQ  195 (196)
Q Consensus       150 ~rR~RT~ft~~Ql~~L~~~F~~~~~p~~~~r~~La~~lgL~~~~Vq  195 (196)
                      +||.||.||..|+.+|+..|..++||+...+++||..+||++.+|+
T Consensus         2 krr~Rt~ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~l~L~~~~V~   47 (68)
T d1ftta_           2 RRKRRVLFSQAQVYELERRFKQQKYLSAPEREHLASMIHLTPTQVK   47 (68)
T ss_dssp             CSSSCSSCCHHHHHHHHHHHHHSSSCCHHHHHHHHHHHTSCHHHHH
T ss_pred             CCCCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHhCCCcccee
Confidence            3678999999999999999999999999999999999999999997

>d1jgga_ a.4.1.1 (A:) Even-skipped homeodomain {Fruit fly (Drosophila melanogaster) [TaxId: 7227]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Even-skipped homeodomain
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

Probab=99.14  E-value=9.3e-12  Score=78.65  Aligned_cols=44  Identities=23%  Similarity=0.319  Sum_probs=42.7

Q ss_pred             hhhcccchhhHhhhhhhhcccCCCChHHHHHHHHHhCcchhhhc
Q psy17504        152 RMRTSFKHHQLRTMKSYFNINQNPDAKDLKQLAQKTGLSKRVLQ  195 (196)
Q Consensus       152 R~RT~ft~~Ql~~L~~~F~~~~~p~~~~r~~La~~lgL~~~~Vq  195 (196)
                      |.||.||..|+.+|+..|+.++||+...+++||..+||++.+||
T Consensus         1 R~Rt~fT~~Ql~~Le~~F~~~~yp~~~~r~~LA~~lgl~~~qV~   44 (57)
T d1jgga_           1 RYRTAFTRDQLGRLEKEFYKENYVSRPRRCELAAQLNLPESTIK   44 (57)
T ss_dssp             CCCCCCCHHHHHHHHHHHHHCSCCCHHHHHHHHHHHTSCHHHHH
T ss_pred             CCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHhCCChhHhh
Confidence            57999999999999999999999999999999999999999997

>d1bw5a_ a.4.1.1 (A:) Insulin gene enhancer protein isl-1 {Rat (Rattus norvegicus) [TaxId: 10116]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Insulin gene enhancer protein isl-1
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=99.11  E-value=1.1e-11  Score=80.57  Aligned_cols=47  Identities=40%  Similarity=0.629  Sum_probs=45.1

Q ss_pred             ccchhhcccchhhHhhhhhhhcccCCCChHHHHHHHHHhCcchhhhc
Q psy17504        149 RTKRMRTSFKHHQLRTMKSYFNINQNPDAKDLKQLAQKTGLSKRVLQ  195 (196)
Q Consensus       149 k~rR~RT~ft~~Ql~~L~~~F~~~~~p~~~~r~~La~~lgL~~~~Vq  195 (196)
                      |.+|.||.||.+|+..|+..|+.|+||+...+++||..+||++.+|+
T Consensus         2 k~kR~Rt~~t~~Q~~~Le~~F~~n~~Ps~~~~~~LA~~l~l~~~~V~   48 (66)
T d1bw5a_           2 KTTRVRTVLNEKQLHTLRTCYAANPRPDALMKEQLVEMTGLSPRVIR   48 (66)
T ss_dssp             CCSCCCCCCSHHHHHHHHHHHHHCSCCCHHHHHHHHHHHTSCHHHHH
T ss_pred             CCCCCCcCcCHHHHHHHHHHHHHCCCCCHHHHHHHHHHcCcCHHHhh
Confidence            46789999999999999999999999999999999999999999996

>d2e1oa1 a.4.1.1 (A:8-64) Homeobox protein prh {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Homeobox protein prh
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.11  E-value=1.7e-11  Score=77.44  Aligned_cols=45  Identities=22%  Similarity=0.290  Sum_probs=43.1

Q ss_pred             chhhcccchhhHhhhhhhhcccCCCChHHHHHHHHHhCcchhhhc
Q psy17504        151 KRMRTSFKHHQLRTMKSYFNINQNPDAKDLKQLAQKTGLSKRVLQ  195 (196)
Q Consensus       151 rR~RT~ft~~Ql~~L~~~F~~~~~p~~~~r~~La~~lgL~~~~Vq  195 (196)
                      |+.||.||..|+.+|+..|+.++||+...+++||..+||++.+|+
T Consensus         1 k~~R~~ft~~Q~~~Le~~F~~n~yp~~~~r~~LA~~l~L~~~qV~   45 (57)
T d2e1oa1           1 KGGQVRFSNDQTIELEKKFETQKYLSPPERKRLAKMLQLSERQVK   45 (57)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTTCCHHHHH
T ss_pred             CCCCccCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCHHHhh
Confidence            467999999999999999999999999999999999999999997

>d1yz8p1 a.4.1.1 (P:1-60) Pituitary homeobox 2 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Pituitary homeobox 2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.10  E-value=1.1e-11  Score=79.02  Aligned_cols=45  Identities=29%  Similarity=0.482  Sum_probs=43.5

Q ss_pred             chhhcccchhhHhhhhhhhcccCCCChHHHHHHHHHhCcchhhhc
Q psy17504        151 KRMRTSFKHHQLRTMKSYFNINQNPDAKDLKQLAQKTGLSKRVLQ  195 (196)
Q Consensus       151 rR~RT~ft~~Ql~~L~~~F~~~~~p~~~~r~~La~~lgL~~~~Vq  195 (196)
                      ||.||.||.+|+..|+..|..++||+...++.||..+||++.+|+
T Consensus         2 rr~Rt~ft~~Q~~~Le~~F~~~~yP~~~~r~~LA~~l~l~~~~V~   46 (60)
T d1yz8p1           2 RRQRTHFTSQQLQQLEATFQRNRYPDMSTREEIAVWTNLTEARVR   46 (60)
T ss_dssp             SCSCCCCCHHHHHHHHHHHTTCSSCCTTTTTHHHHHTTSCHHHHH
T ss_pred             CCCCCCCCHHHHHHHHHHHHHcCCCChHHHHHHHHHHCCChHHHH
Confidence            678999999999999999999999999999999999999999996

>d1b72a_ a.4.1.1 (A:) Homeobox protein hox-b1 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Homeobox protein hox-b1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.08  E-value=2.6e-11  Score=83.11  Aligned_cols=47  Identities=19%  Similarity=0.311  Sum_probs=42.3

Q ss_pred             ccchhhcccchhhHhhhhhhhcccCCCChHHHHHHHHHhCcchhhhc
Q psy17504        149 RTKRMRTSFKHHQLRTMKSYFNINQNPDAKDLKQLAQKTGLSKRVLQ  195 (196)
Q Consensus       149 k~rR~RT~ft~~Ql~~L~~~F~~~~~p~~~~r~~La~~lgL~~~~Vq  195 (196)
                      +++|.||.||..|+..|+..|+.++||+..+|++||..+||++++||
T Consensus        26 ~~kr~Rt~ft~~Ql~~Le~~F~~n~yPs~~~r~~LA~~l~l~~~~V~   72 (88)
T d1b72a_          26 SPSGLRTNFTTRQLTELEKEFHFNKYLSRARRVEIAATLELNETQVK   72 (88)
T ss_dssp             ----CCCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHTCCHHHHH
T ss_pred             CCCCCCcCCCHHHHHHHHHHHHhCCCCchHHHHHHHHHcCCCHHHee
Confidence            45778999999999999999999999999999999999999999996

>d9anta_ a.4.1.1 (A:) Antennapedia Homeodomain {Drosophila melanogaster [TaxId: 7227]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Antennapedia Homeodomain
species: Drosophila melanogaster [TaxId: 7227]

Probab=99.08  E-value=3.2e-11  Score=75.77  Aligned_cols=42  Identities=17%  Similarity=0.316  Sum_probs=41.2

Q ss_pred             hcccchhhHhhhhhhhcccCCCChHHHHHHHHHhCcchhhhc
Q psy17504        154 RTSFKHHQLRTMKSYFNINQNPDAKDLKQLAQKTGLSKRVLQ  195 (196)
Q Consensus       154 RT~ft~~Ql~~L~~~F~~~~~p~~~~r~~La~~lgL~~~~Vq  195 (196)
                      ||.||.+|+..|+..|+.++||+...|++||..+||++++||
T Consensus         1 Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~~V~   42 (56)
T d9anta_           1 RQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIK   42 (56)
T ss_dssp             CCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHTCCHHHHH
T ss_pred             CCcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCChhHee
Confidence            799999999999999999999999999999999999999997

>d1ocpa_ a.4.1.1 (A:) Oct-3 POU Homeodomain {Mouse (Mus musculus) [TaxId: 10090]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Oct-3 POU Homeodomain
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.05  E-value=4.7e-11  Score=77.74  Aligned_cols=47  Identities=26%  Similarity=0.435  Sum_probs=44.3

Q ss_pred             ccchhhcccchhhHhhhhhhhcccCCCChHHHHHHHHHhCcchhhhc
Q psy17504        149 RTKRMRTSFKHHQLRTMKSYFNINQNPDAKDLKQLAQKTGLSKRVLQ  195 (196)
Q Consensus       149 k~rR~RT~ft~~Ql~~L~~~F~~~~~p~~~~r~~La~~lgL~~~~Vq  195 (196)
                      .+||.||.|+..|+..|+..|..++||+...+++||..+||++.+|+
T Consensus         7 ~~rr~Rt~~t~~q~~~Le~~F~~n~~P~~~~r~~La~~~~l~~~~V~   53 (67)
T d1ocpa_           7 ARKRKRTSIENRVRWSLETMFLKCPKPSLQQITHIANQLGLEKDVVR   53 (67)
T ss_dssp             CSSSCCSSCCHHHHHHHHHHHSSCSCCCHHHHHHHHHHHTCCHHHHH
T ss_pred             ccCCCCCCCCHHHHHHHHHHHHHccCCCHHHHHHHHHHHcCCHHHHH
Confidence            34678999999999999999999999999999999999999999996

>d1s7ea1 a.4.1.1 (A:103-152) Hepatocyte nuclear factor 6 {Mouse (Mus musculus) [TaxId: 10090]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Hepatocyte nuclear factor 6
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.05  E-value=3.3e-11  Score=74.05  Aligned_cols=44  Identities=27%  Similarity=0.380  Sum_probs=42.2

Q ss_pred             hhcccchhhHhhhhhhhcccCCCChHHHHHHHHHhCcchhhhcC
Q psy17504        153 MRTSFKHHQLRTMKSYFNINQNPDAKDLKQLAQKTGLSKRVLQN  196 (196)
Q Consensus       153 ~RT~ft~~Ql~~L~~~F~~~~~p~~~~r~~La~~lgL~~~~Vq~  196 (196)
                      +||.||..|+..|+..|+.++||+...+.+||..+||++.+|++
T Consensus         1 PRt~ft~~Q~~~Le~~F~~n~~P~~~~~~~LA~~l~l~~~~V~~   44 (50)
T d1s7ea1           1 PRLVFTDVQRRTLHAIFKENKRPSKELQITISQQLGLELSTVSN   44 (50)
T ss_dssp             CCSCCCHHHHHHHHHHTTSSCSSTHHHHHHHHTTSCSSSHHHHH
T ss_pred             CCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHHCcCHHHhhh
Confidence            58999999999999999999999999999999999999999973

>d1wi3a_ a.4.1.1 (A:) DNA-binding protein SATB2 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: DNA-binding protein SATB2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.02  E-value=5.2e-11  Score=78.42  Aligned_cols=48  Identities=21%  Similarity=0.392  Sum_probs=43.9

Q ss_pred             ccchhhcccchhhHhhhhhhhc-ccCCCChHHHHHHHHHhCcchhhhcC
Q psy17504        149 RTKRMRTSFKHHQLRTMKSYFN-INQNPDAKDLKQLAQKTGLSKRVLQN  196 (196)
Q Consensus       149 k~rR~RT~ft~~Ql~~L~~~F~-~~~~p~~~~r~~La~~lgL~~~~Vq~  196 (196)
                      ..+|.||.|+.+|+..|+..|+ .++||+..++++||..+||++++|++
T Consensus         6 ~~~r~R~~~t~~Q~~~Le~~F~~~~~~P~~~~~~~La~~lgl~~~qV~~   54 (71)
T d1wi3a_           6 SGPRSRTKISLEALGILQSFIHDVGLYPDQEAIHTLSAQLDLPKHTIIK   54 (71)
T ss_dssp             CCCCCCCCCCSHHHHHHHHHHHHHCSCCCHHHHHHHHHHSCCCHHHHHH
T ss_pred             CCCCCCccCCHHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCHHHHHH
Confidence            3467899999999999999997 59999999999999999999999973

>d1uhsa_ a.4.1.1 (A:) Homeodomain-only protein, Hop {Mouse (Mus musculus) [TaxId: 10090]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Homeodomain-only protein, Hop
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=98.95  E-value=1.7e-10  Score=75.98  Aligned_cols=45  Identities=24%  Similarity=0.400  Sum_probs=42.4

Q ss_pred             chhhcccchhhHhhhhhhhcc-cCCCChHHHHHHHHHhCcchhhhc
Q psy17504        151 KRMRTSFKHHQLRTMKSYFNI-NQNPDAKDLKQLAQKTGLSKRVLQ  195 (196)
Q Consensus       151 rR~RT~ft~~Ql~~L~~~F~~-~~~p~~~~r~~La~~lgL~~~~Vq  195 (196)
                      ++.|+.||.+|+..|+..|++ ++||+...|++||..+||++++||
T Consensus         2 ~~~r~~fT~~Ql~~Le~~F~~~n~yP~~~~r~~LA~~lgL~~~~Vq   47 (72)
T d1uhsa_           2 SEGAATMTEDQVEILEYNFNKVNKHPDPTTLCLIAAEAGLTEEQTQ   47 (72)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHSSCSSCCHHHHHHHHHHHTCCHHHHH
T ss_pred             CCCCCCCCHHHHHHHHHHHHHccccCCHHHHHHHHHHhCCCHHHHH
Confidence            567999999999999999986 789999999999999999999997

>d1au7a1 a.4.1.1 (A:103-160) Pit-1 POU homeodomain {Rat (Rattus norvegicus) [TaxId: 10116]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Pit-1 POU homeodomain
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=98.92  E-value=2.6e-10  Score=72.05  Aligned_cols=44  Identities=18%  Similarity=0.397  Sum_probs=42.5

Q ss_pred             hhhcccchhhHhhhhhhhcccCCCChHHHHHHHHHhCcchhhhc
Q psy17504        152 RMRTSFKHHQLRTMKSYFNINQNPDAKDLKQLAQKTGLSKRVLQ  195 (196)
Q Consensus       152 R~RT~ft~~Ql~~L~~~F~~~~~p~~~~r~~La~~lgL~~~~Vq  195 (196)
                      |.||.|+..|+..|+..|+.++||+...+.+||..+||++.+|+
T Consensus         1 r~Rt~~s~~q~~~Le~~F~~~~~P~~~~~~~La~~l~l~~~~V~   44 (58)
T d1au7a1           1 KRRTTISIAAKDALERHFGEHSKPSSQEIMRMAEELNLEKEVVR   44 (58)
T ss_dssp             CCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHH
T ss_pred             CCCCCCCHHHHHHHHHHHHHccCCCHHHHHHHHHHhCCCHHHHH
Confidence            47999999999999999999999999999999999999999997

>d1le8a_ a.4.1.1 (A:) Mating type protein A1 Homeodomain {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Mating type protein A1 Homeodomain
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=98.90  E-value=3.6e-10  Score=70.07  Aligned_cols=43  Identities=16%  Similarity=0.301  Sum_probs=41.4

Q ss_pred             hcccchhhHhhhhhhhcccCCCChHHHHHHHHHhCcchhhhcC
Q psy17504        154 RTSFKHHQLRTMKSYFNINQNPDAKDLKQLAQKTGLSKRVLQN  196 (196)
Q Consensus       154 RT~ft~~Ql~~L~~~F~~~~~p~~~~r~~La~~lgL~~~~Vq~  196 (196)
                      ||.||.+|+..|+..|..++||+...+++||..+||++.+||.
T Consensus         1 Rt~~s~~q~~~Le~~F~~~~~P~~~~~~~LA~~lgl~~~qV~~   43 (53)
T d1le8a_           1 KSSISPQARAFLEQVFRRKQSLNSKEKEEVAKKCGITPLQVRV   43 (53)
T ss_dssp             CCCCCHHHHHHHHHHHHHCSCCCHHHHHHHHHHTTSCHHHHHH
T ss_pred             CCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHCCCHHHHHH
Confidence            7899999999999999999999999999999999999999973

>d2cufa1 a.4.1.1 (A:8-89) Homeobox-containing protein 1, HMBOX1 (Flj21616) {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Homeobox-containing protein 1, HMBOX1 (Flj21616)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.85  E-value=4.7e-10  Score=75.73  Aligned_cols=45  Identities=27%  Similarity=0.441  Sum_probs=41.4

Q ss_pred             chhhcccchhhHhhhhhhhcccCCCChHHHHHHHHHhC---------------cchhhhc
Q psy17504        151 KRMRTSFKHHQLRTMKSYFNINQNPDAKDLKQLAQKTG---------------LSKRVLQ  195 (196)
Q Consensus       151 rR~RT~ft~~Ql~~L~~~F~~~~~p~~~~r~~La~~lg---------------L~~~~Vq  195 (196)
                      ||.||.||..||.+|+..|+.++||+...|++||..+|               |++.+|+
T Consensus         1 Rr~R~~ft~~Ql~~LE~~F~~n~yP~~~~R~~LA~~~~~~~~~~~~~~~~~~~l~~~~V~   60 (82)
T d2cufa1           1 RGSRFTWRKECLAVMESYFNENQYPDEAKREEIANACNAVIQKPGKKLSDLERVTSLKVY   60 (82)
T ss_dssp             CCCSCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHHHHHCCTTCCCCTTTCCCHHHHH
T ss_pred             CcCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhccccccccccchhccCCCHHHHH
Confidence            57899999999999999999999999999999999886               7777776

>d1e3oc1 a.4.1.1 (C:104-160) Oct-1 POU Homeodomain {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Oct-1 POU Homeodomain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.79  E-value=1.4e-09  Score=68.30  Aligned_cols=43  Identities=26%  Similarity=0.427  Sum_probs=41.6

Q ss_pred             hhcccchhhHhhhhhhhcccCCCChHHHHHHHHHhCcchhhhc
Q psy17504        153 MRTSFKHHQLRTMKSYFNINQNPDAKDLKQLAQKTGLSKRVLQ  195 (196)
Q Consensus       153 ~RT~ft~~Ql~~L~~~F~~~~~p~~~~r~~La~~lgL~~~~Vq  195 (196)
                      .||.|+..|+..|+..|+.++||+...+++||..+||++.+|+
T Consensus         1 kRT~~~~~q~~~Le~~F~~~~~P~~~~~~~LA~~lgL~~~qV~   43 (57)
T d1e3oc1           1 KRTSIETNIRVALEKSFMENQKPTSEDITLIAEQLNMEKEVIR   43 (57)
T ss_dssp             CCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHH
T ss_pred             CCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHHCCCHHHHH
Confidence            4899999999999999999999999999999999999999997

>d1pufb_ a.4.1.1 (B:) pbx1 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: pbx1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.69  E-value=3.7e-09  Score=69.66  Aligned_cols=46  Identities=26%  Similarity=0.512  Sum_probs=42.4

Q ss_pred             chhhcccchhhHhhhhhhhc---ccCCCChHHHHHHHHHhCcchhhhcC
Q psy17504        151 KRMRTSFKHHQLRTMKSYFN---INQNPDAKDLKQLAQKTGLSKRVLQN  196 (196)
Q Consensus       151 rR~RT~ft~~Ql~~L~~~F~---~~~~p~~~~r~~La~~lgL~~~~Vq~  196 (196)
                      ||.|+.|+.+|+..|+..|.   .++||+..++++||..+||++.+|++
T Consensus         2 rk~R~~~t~~q~~~Le~~f~~~~~~pYPs~~~k~~La~~~gl~~~qv~~   50 (73)
T d1pufb_           2 RRKRRNFNKQATEILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSN   50 (73)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHHTTTSCCCCHHHHHHHHHHHTSCHHHHHH
T ss_pred             CCCCCCCCHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHCcCHHHhHH
Confidence            56789999999999999997   48899999999999999999999973

>d2ecca1 a.4.1.1 (A:1-76) Homeobox-leucine zipper protein Homez {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Homeobox-leucine zipper protein Homez
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.52  E-value=1.7e-08  Score=66.85  Aligned_cols=41  Identities=29%  Similarity=0.357  Sum_probs=38.7

Q ss_pred             ccchhhHhhhhhhhcccCCCChHHHHHHHHHhCcchhhhcC
Q psy17504        156 SFKHHQLRTMKSYFNINQNPDAKDLKQLAQKTGLSKRVLQN  196 (196)
Q Consensus       156 ~ft~~Ql~~L~~~F~~~~~p~~~~r~~La~~lgL~~~~Vq~  196 (196)
                      .||.+|+..|+..|..++||+..+++.||..|||++.+|++
T Consensus         9 r~T~eQ~~~Le~~F~~n~~Ps~~~~~~La~~~gL~~~qV~~   49 (76)
T d2ecca1           9 RKTKEQLAILKSFFLQCQWARREDYQKLEQITGLPRPEIIQ   49 (76)
T ss_dssp             CCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTCCCHHHHHH
T ss_pred             CCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHHccCHHHHHH
Confidence            46899999999999999999999999999999999999973

>d1lfba_ a.4.1.1 (A:) Hepatocyte nuclear factor 1a (LFB1/HNF1) {Rat (Rattus rattus) [TaxId: 10117]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Hepatocyte nuclear factor 1a (LFB1/HNF1)
species: Rat (Rattus rattus) [TaxId: 10117]

Probab=98.51  E-value=1.9e-08  Score=66.95  Aligned_cols=36  Identities=11%  Similarity=0.234  Sum_probs=34.3

Q ss_pred             hcccchhhHhhhhhhhcccCCCChHHHHHHHHHhCc
Q psy17504        154 RTSFKHHQLRTMKSYFNINQNPDAKDLKQLAQKTGL  189 (196)
Q Consensus       154 RT~ft~~Ql~~L~~~F~~~~~p~~~~r~~La~~lgL  189 (196)
                      |+.||..|+..|+..|+.++||+...|+.||..+++
T Consensus         1 R~~~tp~Ql~~Le~~F~~n~yPs~~~Re~LA~~ln~   36 (78)
T d1lfba_           1 RFKWGPASQQILFQAYERQKNPSKEERETLVEECNR   36 (78)
T ss_dssp             CCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHHH
T ss_pred             CccCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhch
Confidence            689999999999999999999999999999999963

>d2ecba1 a.4.1.1 (A:8-83) Zinc fingers and homeoboxes protein 1, ZHX1 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Zinc fingers and homeoboxes protein 1, ZHX1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.51  E-value=2.6e-08  Score=65.96  Aligned_cols=39  Identities=23%  Similarity=0.341  Sum_probs=37.5

Q ss_pred             cchhhHhhhhhhhcccCCCChHHHHHHHHHhCcchhhhc
Q psy17504        157 FKHHQLRTMKSYFNINQNPDAKDLKQLAQKTGLSKRVLQ  195 (196)
Q Consensus       157 ft~~Ql~~L~~~F~~~~~p~~~~r~~La~~lgL~~~~Vq  195 (196)
                      +|.+|+..|+..|..++||+...+++||..+||++++|+
T Consensus        11 ~T~~Q~~~Le~~F~~~~~P~~~~r~~LA~~l~l~~~~V~   49 (76)
T d2ecba1          11 KTAEQLRVLQASFLNSSVLTDEELNRLRAQTKLTRREID   49 (76)
T ss_dssp             CCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTCCCHHHHH
T ss_pred             CCHHHHHHHHHHHHHCCCCCHHHHHHHHHHhCCCHHHHH
Confidence            478999999999999999999999999999999999997

>d1x2na1 a.4.1.1 (A:6-67) Homeobox protein pknox1 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Homeobox protein pknox1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.44  E-value=4.2e-08  Score=62.39  Aligned_cols=46  Identities=26%  Similarity=0.374  Sum_probs=41.6

Q ss_pred             chhhcccchhhHhhhhhhhcc---cCCCChHHHHHHHHHhCcchhhhcC
Q psy17504        151 KRMRTSFKHHQLRTMKSYFNI---NQNPDAKDLKQLAQKTGLSKRVLQN  196 (196)
Q Consensus       151 rR~RT~ft~~Ql~~L~~~F~~---~~~p~~~~r~~La~~lgL~~~~Vq~  196 (196)
                      |+.|+.|+.+|+..|+..|..   ++||+..+++.||..+||+..||++
T Consensus         3 krkR~~~~~~~~~iL~~wf~~~~~nPyPs~~e~~~La~~~~l~~~qI~~   51 (62)
T d1x2na1           3 KNKRGVLPKHATNVMRSWLFQHIGHPYPTEDEKKQIAAQTNLTLLQVNN   51 (62)
T ss_dssp             CCSSCCCCHHHHHHHHHHHHHTTTSCCCCHHHHHHHHHHHTCCHHHHHH
T ss_pred             CCCCCCCCHHHHHHHHHHHHHhccCCCcCHHHHHHHHHHHCcCHHHhHH
Confidence            445788999999999999984   8899999999999999999999974

>d1g47a2 g.39.1.3 (A:36-70) Pinch (particularly interesting new Cys-His) protein {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Pinch (particularly interesting new Cys-His) protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.30  E-value=4.4e-08  Score=55.07  Aligned_cols=33  Identities=24%  Similarity=0.502  Sum_probs=29.9

Q ss_pred             hhhhhhcceeccCCccccccceeeeccchhhhhh
Q psy17504         22 FTCISCGILLTKGDLFGMRDEMIYCRPHYEILRH   55 (196)
Q Consensus        22 F~C~~C~~~L~~G~~f~~~~~~~~C~~~y~~~~~   55 (196)
                      |+|..|+++| .+..|..++|++||..||+.+++
T Consensus         1 F~C~~C~~~f-~~~~F~e~~G~pYCe~~Y~~lFA   33 (35)
T d1g47a2           1 FVCAQCFQQF-PEGLFYEFEGRKYCEHDFQMLFA   33 (35)
T ss_dssp             CCCTTTCCCC-GGGCSEEETTEEECHHHHHHHCC
T ss_pred             CCCCCCcCCC-CCCCeEEECCEecChHhHHhhcC
Confidence            7899999999 46788889999999999999985

>d1rutx3 g.39.1.3 (X:83-113) LIM only 4 (Lmo4) {Mouse (Mus musculus) [TaxId: 10090]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: LIM only 4 (Lmo4)
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=98.29  E-value=2.1e-09  Score=58.31  Aligned_cols=22  Identities=59%  Similarity=0.995  Sum_probs=20.5

Q ss_pred             CCCChHHHHHHHHhHHHhhhhh
Q psy17504          1 MGISSSELVMRARDLVFHLHCF   22 (196)
Q Consensus         1 ~~i~~~~~v~~a~~~~~H~~CF   22 (196)
                      .+|.++|+||||++++||+.||
T Consensus        10 ~~I~~~e~VmRA~~~VyHl~CF   31 (31)
T d1rutx3          10 QSIPASELVMRAQGNVYHLKCF   31 (31)
T ss_dssp             CEECTTSEEEEETTEEECGGGC
T ss_pred             CcCChhHhheecccceeeeccC
Confidence            3689999999999999999998

>d1k61a_ a.4.1.1 (A:) mat alpha2 Homeodomain {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: mat alpha2 Homeodomain
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=98.27  E-value=1.7e-07  Score=59.05  Aligned_cols=40  Identities=33%  Similarity=0.547  Sum_probs=37.1

Q ss_pred             cchhhHhhhhhhhccc---CCCChHHHHHHHHHhCcchhhhcC
Q psy17504        157 FKHHQLRTMKSYFNIN---QNPDAKDLKQLAQKTGLSKRVLQN  196 (196)
Q Consensus       157 ft~~Ql~~L~~~F~~~---~~p~~~~r~~La~~lgL~~~~Vq~  196 (196)
                      |+.+|+..|+..|..+   +||+..++++||..+||++.+|++
T Consensus         5 ft~~q~~~L~~~f~~~~~~pyPs~~e~~~La~~~gL~~~qV~~   47 (60)
T d1k61a_           5 FTKENVRILESWFAKNIENPYLDTKGLENLMKNTSLSRIQIKN   47 (60)
T ss_dssp             CCHHHHHHHHHHHHHTTTSCCCCHHHHHHHHHHHCCCHHHHHH
T ss_pred             CCHHHHHHHHHHHHHcCCCCCcCHHHHHHHHHHHCcCHHHHhH
Confidence            8999999999999764   799999999999999999999973

>d2cqxa1 a.4.1.1 (A:8-66) LAG1 longevity assurance homolog 5, LASS5 {Mouse (Mus musculus) [TaxId: 10090]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: LAG1 longevity assurance homolog 5, LASS5
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=98.24  E-value=2.1e-07  Score=58.48  Aligned_cols=44  Identities=27%  Similarity=0.299  Sum_probs=40.0

Q ss_pred             hhhcccchhhHhhhhhhhcc-cCCCChHHHHHHHHHhCcchhhhc
Q psy17504        152 RMRTSFKHHQLRTMKSYFNI-NQNPDAKDLKQLAQKTGLSKRVLQ  195 (196)
Q Consensus       152 R~RT~ft~~Ql~~L~~~F~~-~~~p~~~~r~~La~~lgL~~~~Vq  195 (196)
                      +.++.++.+|...||..|.. ++||+...+++||..+||++++|+
T Consensus         3 k~~~~~k~~~~~iLE~~F~~~~~yPs~~~~~~LA~~lgls~~qV~   47 (59)
T d2cqxa1           3 KDSPVNKVEPNDTLEKVFVSVTKYPDEKRLKGLSKQLDWSVRKIQ   47 (59)
T ss_dssp             CCCCCSCSCSTTHHHHHHHHTCSSCCHHHHHHHHHHTTCCHHHHH
T ss_pred             CCCCCCCccccHHHHHHHHHcCCCcCHHHHHHHHHHHCcCHHHHH
Confidence            35678889999999999986 689999999999999999999997

>d1x2ma1 a.4.1.1 (A:8-59) Lag1 longevity assurance homolog 6, LASS6 {Mouse (Mus musculus) [TaxId: 10090]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Lag1 longevity assurance homolog 6, LASS6
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=98.19  E-value=4.6e-07  Score=55.40  Aligned_cols=38  Identities=21%  Similarity=0.375  Sum_probs=35.4

Q ss_pred             chhhHhhhhhhhcc-cCCCChHHHHHHHHHhCcchhhhc
Q psy17504        158 KHHQLRTMKSYFNI-NQNPDAKDLKQLAQKTGLSKRVLQ  195 (196)
Q Consensus       158 t~~Ql~~L~~~F~~-~~~p~~~~r~~La~~lgL~~~~Vq  195 (196)
                      |.+|+..||..|.. ++||+...++.||..+||++++|+
T Consensus         1 T~~q~~iLE~~F~~~~~~P~~~~~~~LA~~~~ls~~qV~   39 (52)
T d1x2ma1           1 TAQPNAILEKVFTAITKHPDEKRLEGLSKQLDWDVRSIQ   39 (52)
T ss_dssp             SSCHHHHHHHHHHTTCSSCCHHHHHHHHHHHCSCHHHHH
T ss_pred             ChhHHHHHHHHHHHcCCCcCHHHHHHHHHHHCcCHHHHH
Confidence            56899999999976 799999999999999999999997

>d1rutx4 g.39.1.3 (X:114-146) LIM only 4 (Lmo4) {Mouse (Mus musculus) [TaxId: 10090]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: LIM only 4 (Lmo4)
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=97.95  E-value=1.2e-06  Score=46.72  Aligned_cols=29  Identities=28%  Similarity=0.592  Sum_probs=26.6

Q ss_pred             hhhhhcceeccCCccccccceeeeccchh
Q psy17504         23 TCISCGILLTKGDLFGMRDEMIYCRPHYE   51 (196)
Q Consensus        23 ~C~~C~~~L~~G~~f~~~~~~~~C~~~y~   51 (196)
                      +|.+|..+|.+|+.|...+|.+||+.|-.
T Consensus         1 tC~tC~n~LVPGDRFHyvNG~lfCE~D~p   29 (33)
T d1rutx4           1 TCSTCRNRLVPGDRFHYINGSLFCEHDRP   29 (33)
T ss_dssp             BCTTTCCBCCTTCEEEEETTEEEEGGGCC
T ss_pred             CcccccccccCCceeEEecCEEEEecCCc
Confidence            59999999999999999999999998854

>d1u5sb2 g.39.1.3 (B:103-137) Pinch (particularly interesting new Cys-His) protein {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Pinch (particularly interesting new Cys-His) protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.77  E-value=2.4e-06  Score=46.29  Aligned_cols=33  Identities=30%  Similarity=0.617  Sum_probs=30.2

Q ss_pred             hhhhhhcceeccCCccccccceeeeccchhhhhh
Q psy17504         22 FTCISCGILLTKGDLFGMRDEMIYCRPHYEILRH   55 (196)
Q Consensus        22 F~C~~C~~~L~~G~~f~~~~~~~~C~~~y~~~~~   55 (196)
                      |.|..|.+++ .|...+.+.|..||+.||++||.
T Consensus         1 FvCA~CekPF-~G~rhyE~~g~ayCe~Hy~qLfg   33 (35)
T d1u5sb2           1 FVCAKCEKPF-LGHRHYERKGLAYCETHYNQLFG   33 (35)
T ss_dssp             CBCTTTCCBC-SSSCCEEETTEEECHHHHHHHCS
T ss_pred             CcccccCCcc-CCchhhhhcCchHHHHHHHHHhc
Confidence            7899999999 68888889999999999999984

>d2d8za2 g.39.1.3 (A:33-64) Four and a half LIM domains protein 2, FHL2 {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Four and a half LIM domains protein 2, FHL2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.76  E-value=2.2e-06  Score=46.32  Aligned_cols=30  Identities=33%  Similarity=0.686  Sum_probs=28.0

Q ss_pred             hhhhcceeccCCccccccceeeeccchhhhh
Q psy17504         24 CISCGILLTKGDLFGMRDEMIYCRPHYEILR   54 (196)
Q Consensus        24 C~~C~~~L~~G~~f~~~~~~~~C~~~y~~~~   54 (196)
                      |..|.++| .|..|.++++++||-.+|..++
T Consensus         2 C~~C~~~L-~GQry~~rd~~PyC~~Cf~~lf   31 (32)
T d2d8za2           2 CTACRKQL-SGQRFTARDDFAYCLNCFCDLY   31 (32)
T ss_dssp             CSSSCCBC-TTSCCEESSSSEECHHHHHHHT
T ss_pred             cccCCccc-cCceeeecCCCeehHHhhHhhc
Confidence            78899999 7999999999999999999886

>d2dj7a1 g.39.1.3 (A:44-74) Actin-binding LIM protein 3, abLIM-3 {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Actin-binding LIM protein 3, abLIM-3
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.71  E-value=4.2e-06  Score=44.61  Aligned_cols=30  Identities=23%  Similarity=0.648  Sum_probs=25.8

Q ss_pred             hhhhhcceeccCCccccccceeeeccchhhhh
Q psy17504         23 TCISCGILLTKGDLFGMRDEMIYCRPHYEILR   54 (196)
Q Consensus        23 ~C~~C~~~L~~G~~f~~~~~~~~C~~~y~~~~   54 (196)
                      +|..|++.| . .+|..++|.+||..||+..|
T Consensus         1 kC~~C~~vL-~-gEYm~kdG~PyCe~DY~~~F   30 (31)
T d2dj7a1           1 KCQTCSVIL-T-GEYISKDGVPYCESDYHAQF   30 (31)
T ss_dssp             BCSSSCCBC-S-SCCEEETTEEECTTHHHHHT
T ss_pred             CccccCccc-c-ceeecCCCCcccHHHHHHhc
Confidence            488999999 3 47777999999999999876

>d2d8ya2 g.39.1.3 (A:44-85) Eplin, LIMA1 {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Eplin, LIMA1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.69  E-value=4.4e-06  Score=48.24  Aligned_cols=36  Identities=28%  Similarity=0.582  Sum_probs=29.8

Q ss_pred             hhhhhcceeccCCccccccceeeeccchhhhhhcccc
Q psy17504         23 TCISCGILLTKGDLFGMRDEMIYCRPHYEILRHRDYC   59 (196)
Q Consensus        23 ~C~~C~~~L~~G~~f~~~~~~~~C~~~y~~~~~~~~~   59 (196)
                      +|..|++.|+.| .|...+|.+||+.||.+||...+.
T Consensus         1 rC~~C~~~Ls~~-~yas~~G~lYCkpHf~qLF~~kGn   36 (42)
T d2d8ya2           1 RCSYCNNKLSLG-TYASLHGRIYCKPHFNQLFKSKGN   36 (42)
T ss_dssp             BCTTTCCBCCTT-TCCCSSSCCCCHHHHHHHSCCCSC
T ss_pred             CcCcCCCCccCC-cchhhCCEeccHHHHHHHHHhhcC
Confidence            589999999776 555569999999999999976543

>d1x3ha2 g.39.1.3 (A:43-74) Leupaxin {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Leupaxin
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.67  E-value=3.8e-06  Score=45.59  Aligned_cols=31  Identities=26%  Similarity=0.394  Sum_probs=26.2

Q ss_pred             hhhhhcceeccCCccccccceeeeccchhhhh
Q psy17504         23 TCISCGILLTKGDLFGMRDEMIYCRPHYEILR   54 (196)
Q Consensus        23 ~C~~C~~~L~~G~~f~~~~~~~~C~~~y~~~~   54 (196)
                      .|..|.+++ .+..|+..+|++||..||+.+.
T Consensus         1 VC~~C~~PF-~~~~Fy~~~g~PyCe~HyH~~~   31 (32)
T d1x3ha2           1 VCGDCFTSF-STGSFFELDGRPFCELHYHHRR   31 (32)
T ss_dssp             BCSSSCCBS-CSSCCEESSSCEECHHHHHHHH
T ss_pred             CcCccCCcC-CCCCeEeECCccchHHhhhhhc
Confidence            488999999 5667777899999999998764

>d2cuqa1 g.39.1.3 (A:43-74) Four and a half LIM domains 3, FHL3 {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Four and a half LIM domains 3, FHL3
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.56  E-value=7.2e-06  Score=43.76  Aligned_cols=31  Identities=35%  Similarity=0.635  Sum_probs=28.5

Q ss_pred             hhhhhcceeccCCccccccceeeeccchhhhh
Q psy17504         23 TCISCGILLTKGDLFGMRDEMIYCRPHYEILR   54 (196)
Q Consensus        23 ~C~~C~~~L~~G~~f~~~~~~~~C~~~y~~~~   54 (196)
                      .|..|+++| .|..|..++.++||-.||..|+
T Consensus         1 vCt~Ck~~L-aGqrFTSrde~pYC~~Cfg~Lf   31 (32)
T d2cuqa1           1 VCTGCQTPL-AGQQFTSRDEDPYCVACFGELF   31 (32)
T ss_dssp             BCSSSCCBC-TTCCEEECSSSEEEHHHHHHHT
T ss_pred             CccccCccc-cCCccccCCCCccHHHHhHhhc
Confidence            388999999 8999999999999999998876

>d1ibia2 g.39.1.3 (A:145-175) Cysteine-rich (intestinal) protein, CRP, CRIP {Japanese quail (Coturnix coturnix japonica), CRP2 [TaxId: 93934]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Cysteine-rich (intestinal) protein, CRP, CRIP
species: Japanese quail (Coturnix coturnix japonica), CRP2 [TaxId: 93934]

Probab=97.25  E-value=2.4e-05  Score=40.85  Aligned_cols=30  Identities=30%  Similarity=0.734  Sum_probs=25.1

Q ss_pred             hhhhhhcceeccCCccccccceeeeccchhh
Q psy17504         22 FTCISCGILLTKGDLFGMRDEMIYCRPHYEI   52 (196)
Q Consensus        22 F~C~~C~~~L~~G~~f~~~~~~~~C~~~y~~   52 (196)
                      |+|..|++-| ......-++|.+||+.||..
T Consensus         1 frca~cgk~l-estt~adkdgeiyck~cyak   30 (31)
T d1ibia2           1 FRCAKCGKSL-ESTTLTEKEGEIYCKGCYAK   30 (31)
T ss_dssp             EECSSSCCEE-CSSCSEEETTEEECHHHHHH
T ss_pred             CccccccCcc-ccceeeccCCcEEEeeeeec
Confidence            7899999999 55566668999999999853

>d1b8ta4 g.39.1.3 (A:144-192) Cysteine-rich (intestinal) protein, CRP, CRIP {Chicken (Gallus gallus) [TaxId: 9031]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Cysteine-rich (intestinal) protein, CRP, CRIP
species: Chicken (Gallus gallus) [TaxId: 9031]

Probab=97.13  E-value=6.7e-05  Score=44.56  Aligned_cols=34  Identities=26%  Similarity=0.501  Sum_probs=28.3

Q ss_pred             hhhhhcceeccCCccccccceeeeccchhhhhhcc
Q psy17504         23 TCISCGILLTKGDLFGMRDEMIYCRPHYEILRHRD   57 (196)
Q Consensus        23 ~C~~C~~~L~~G~~f~~~~~~~~C~~~y~~~~~~~   57 (196)
                      +|..|++.|..+ ....+++++||+.||..+|.+.
T Consensus         1 KC~~C~k~Lds~-t~~ehdg~~YCk~CY~k~fGPK   34 (49)
T d1b8ta4           1 RCAKCGKSLEST-TLADKDGEIYCKGCYAKNFGPK   34 (49)
T ss_dssp             BCTTTCCBCCSS-SEEEETTEEEEHHHHHHHTCCC
T ss_pred             ChhhcCCccCCC-cccccCCcccchhhhhhccCCC
Confidence            489999999765 4455899999999999999754

>d2dloa2 g.39.1.3 (A:43-75) Thyroid receptor interacting protein 6, TRIP6 {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Thyroid receptor interacting protein 6, TRIP6
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.09  E-value=4.8e-05  Score=41.16  Aligned_cols=31  Identities=26%  Similarity=0.425  Sum_probs=27.3

Q ss_pred             hhhhhcceeccCCccccc-cceeeeccchhhhh
Q psy17504         23 TCISCGILLTKGDLFGMR-DEMIYCRPHYEILR   54 (196)
Q Consensus        23 ~C~~C~~~L~~G~~f~~~-~~~~~C~~~y~~~~   54 (196)
                      +|.+|++.| .|-.|.+. .+++||-.||+..+
T Consensus         1 tCvvC~~~L-DGvPFtvD~~n~i~Cv~DyHrkf   32 (33)
T d2dloa2           1 TCVVCHRGL-DGIPFTVDATSQIHCIEDFHRKF   32 (33)
T ss_dssp             BCSSSCCBC-TTSCEECCTTCCCEEHHHHHHHT
T ss_pred             CeeEcCccc-CCCcEEEcCCCCEeehhhhhhhc
Confidence            589999999 89999886 58999999999865

>d1x61a2 g.39.1.3 (A:35-66) Thyroid receptor interacting protein 6, TRIP6 {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Thyroid receptor interacting protein 6, TRIP6
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.87  E-value=9.7e-05  Score=38.93  Aligned_cols=29  Identities=28%  Similarity=0.626  Sum_probs=25.7

Q ss_pred             hhhhhcceeccCCccccccceeeeccchhh
Q psy17504         23 TCISCGILLTKGDLFGMRDEMIYCRPHYEI   52 (196)
Q Consensus        23 ~C~~C~~~L~~G~~f~~~~~~~~C~~~y~~   52 (196)
                      .|.+|+..| .|..|+-.+.+-||+.||..
T Consensus         1 vC~tC~~kL-RGqpFYAvekkayCE~CYi~   29 (32)
T d1x61a2           1 VCSTCRAQL-RGQHFYAVERRAYCEGCYVA   29 (32)
T ss_dssp             BCSSSCCBC-TTSCEEESSSCEEEHHHHHH
T ss_pred             CeeEeCcee-cCCcceEeeccccccceeee
Confidence            388999999 68889888999999999964

>d2cura1 g.39.1.3 (A:33-63) Four and a half LIM domains protein 1, FHL-1 {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Four and a half LIM domains protein 1, FHL-1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.73  E-value=0.00019  Score=37.67  Aligned_cols=29  Identities=28%  Similarity=0.702  Sum_probs=26.1

Q ss_pred             hhhhhcceeccCCccccccceeeeccchhh
Q psy17504         23 TCISCGILLTKGDLFGMRDEMIYCRPHYEI   52 (196)
Q Consensus        23 ~C~~C~~~L~~G~~f~~~~~~~~C~~~y~~   52 (196)
                      .|..|.+.| .|..|...+.++||-.||..
T Consensus         1 vC~~C~K~L-ag~rFTa~eDq~yCVdCYK~   29 (31)
T d2cura1           1 VCVTCSKKL-AGQRFTAVEDQYYCVDCYKN   29 (31)
T ss_dssp             BCTTTCCBC-TTSCEEECSSCEEEHHHHHH
T ss_pred             Ccccccchh-cCceeEEecceEEEeeeecc
Confidence            389999999 79999999999999999964

>d1imla2 g.39.1.3 (A:29-76) Cysteine-rich (intestinal) protein, CRP, CRIP {Rat (Rattus rattus) [TaxId: 10117]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Cysteine-rich (intestinal) protein, CRP, CRIP
species: Rat (Rattus rattus) [TaxId: 10117]

Probab=96.59  E-value=0.0004  Score=40.69  Aligned_cols=34  Identities=29%  Similarity=0.595  Sum_probs=28.1

Q ss_pred             hhhhhcceeccCCccccccceeee-ccchhhhhhcc
Q psy17504         23 TCISCGILLTKGDLFGMRDEMIYC-RPHYEILRHRD   57 (196)
Q Consensus        23 ~C~~C~~~L~~G~~f~~~~~~~~C-~~~y~~~~~~~   57 (196)
                      +|..|++.|..| .....++++|| +.||..+|.+.
T Consensus         1 kC~~C~K~L~sg-~~aeHdg~pYC~k~CY~~~FGPk   35 (48)
T d1imla2           1 KCEKCGKTLTSG-GHAEHEGKPYCNHPCYSAMFGPK   35 (48)
T ss_dssp             BCTTTCCBCCTT-TEEEETTEEEETTTHHHHHSSCC
T ss_pred             CchhcCcCcCCC-ChhhcCCcccccccchhhccCCC
Confidence            489999999665 45668999999 88999999754

>d1b8ta2 g.39.1.3 (A:36-100) Cysteine-rich (intestinal) protein, CRP, CRIP {Chicken (Gallus gallus) [TaxId: 9031]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Cysteine-rich (intestinal) protein, CRP, CRIP
species: Chicken (Gallus gallus) [TaxId: 9031]

Probab=96.56  E-value=0.00036  Score=43.62  Aligned_cols=34  Identities=21%  Similarity=0.431  Sum_probs=28.0

Q ss_pred             hhhhcceeccCCccccccceeeeccchhhhhhccc
Q psy17504         24 CISCGILLTKGDLFGMRDEMIYCRPHYEILRHRDY   58 (196)
Q Consensus        24 C~~C~~~L~~G~~f~~~~~~~~C~~~y~~~~~~~~   58 (196)
                      |..|++.|..+ ....+++.+||+.||..+|.+..
T Consensus         2 C~~C~K~LdS~-~~~eh~~e~YCk~CY~k~fGPkG   35 (65)
T d1b8ta2           2 CMVCKKNLDST-TVAVHGDEIYCKSCYGKKYGPKG   35 (65)
T ss_dssp             CTTTCCBCCSS-SEEEETTEEEEHHHHHHHHSCCC
T ss_pred             chhcCCccCCC-ccccCCCcccchhhhccccCCCc
Confidence            88999999544 45667899999999999997543

>d1x6aa2 g.39.1.3 (A:42-75) Lim domain kinase 2 {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Lim domain kinase 2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.54  E-value=0.00028  Score=37.92  Aligned_cols=32  Identities=25%  Similarity=0.803  Sum_probs=28.1

Q ss_pred             hhhhhhcceeccCCcccccc-ceeeeccchhhh
Q psy17504         22 FTCISCGILLTKGDLFGMRD-EMIYCRPHYEIL   53 (196)
Q Consensus        22 F~C~~C~~~L~~G~~f~~~~-~~~~C~~~y~~~   53 (196)
                      |.|..|+.-+..|+.|.+.+ .++||..||.+.
T Consensus         1 F~C~~C~~fIgdgdsyaLVerskLYCG~Cy~~~   33 (34)
T d1x6aa2           1 FACMSCKVIIEDGDAYALVQHATLYCGKCHNEV   33 (34)
T ss_dssp             CBCTTTCCBCCTTSCEEECSSSCEEEHHHHHHH
T ss_pred             CcccccccEEecCceEEEEeeceeeeecchhcc
Confidence            78999999999999998875 699999999753

>d2cu8a2 g.39.1.3 (A:38-70) Cysteine-rich (intestinal) protein, CRP, CRIP {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Cysteine-rich (intestinal) protein, CRP, CRIP
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.50  E-value=0.00033  Score=37.38  Aligned_cols=31  Identities=32%  Similarity=0.628  Sum_probs=25.0

Q ss_pred             hhhhhcceeccCCccccccceeeec-cchhhhh
Q psy17504         23 TCISCGILLTKGDLFGMRDEMIYCR-PHYEILR   54 (196)
Q Consensus        23 ~C~~C~~~L~~G~~f~~~~~~~~C~-~~y~~~~   54 (196)
                      +|..|++.|.+|.. ...+|++||. .||..||
T Consensus         1 kCekC~ktL~~G~H-aEH~gkPYC~~PCY~aLF   32 (33)
T d2cu8a2           1 KCERCSKTLTPGGH-AEHDGKPFCHKPCYATLF   32 (33)
T ss_dssp             BCSSSCCBCCTTSC-EEETTEEECTTTHHHHHS
T ss_pred             CchhcccccCCCCc-cccCCCcCcCcchHHhhc
Confidence            48899999988865 4579999995 5888776

>d1a7ia2 g.39.1.3 (A:36-67) Cysteine-rich (intestinal) protein, CRP, CRIP {Japanese quail (Coturnix coturnix japonica), CRP2 [TaxId: 93934]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Cysteine-rich (intestinal) protein, CRP, CRIP
species: Japanese quail (Coturnix coturnix japonica), CRP2 [TaxId: 93934]

Probab=96.48  E-value=0.00036  Score=36.78  Aligned_cols=29  Identities=24%  Similarity=0.637  Sum_probs=24.9

Q ss_pred             hhhhcceeccCCccccccceeeeccchhhh
Q psy17504         24 CISCGILLTKGDLFGMRDEMIYCRPHYEIL   53 (196)
Q Consensus        24 C~~C~~~L~~G~~f~~~~~~~~C~~~y~~~   53 (196)
                      |.+|++.| ....-..+++.+||+.||...
T Consensus         2 C~~C~K~L-dStTva~h~~eiYCKsCygkk   30 (32)
T d1a7ia2           2 CMVCRKNL-DSTTVAIHDAEVYCKSCYGKK   30 (32)
T ss_dssp             CSSSCCEE-CSSCCEEETTEEECSHHHHHH
T ss_pred             chhhhhcc-CcceeeeecceEEehhhcccc
Confidence            88999999 566777889999999999764

>d2dara1 g.39.1.3 (A:53-84) PDZ and LIM domain protein 5, Enigma {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: PDZ and LIM domain protein 5, Enigma
species: Human (Homo sapiens) [TaxId: 9606]

Probab=95.98  E-value=0.0008  Score=35.72  Aligned_cols=30  Identities=23%  Similarity=0.391  Sum_probs=24.7

Q ss_pred             hhhhcceeccCCccccccceeeeccchhhhh
Q psy17504         24 CISCGILLTKGDLFGMRDEMIYCRPHYEILR   54 (196)
Q Consensus        24 C~~C~~~L~~G~~f~~~~~~~~C~~~y~~~~   54 (196)
                      |..|++.| .---|.-..|.+||..||...+
T Consensus         2 Ca~C~~sL-~d~gFVEE~g~lYCe~Cye~ff   31 (32)
T d2dara1           2 CAHCKNTM-AYIGFVEEKGALYCELCYEKFF   31 (32)
T ss_dssp             CSSSCCBC-SSSCBEESSSCEECHHHHHHHT
T ss_pred             cccccccH-hhcceeeecCcEeHHHHHHHhc
Confidence            88999999 4446777789999999998765

>d1rutx2 g.39.1.3 (X:49-82) LIM only 4 (Lmo4) {Mouse (Mus musculus) [TaxId: 10090]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: LIM only 4 (Lmo4)
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=95.83  E-value=0.00073  Score=36.24  Aligned_cols=32  Identities=34%  Similarity=0.527  Sum_probs=26.6

Q ss_pred             hhhhhcceecc-CCccccccceeeeccchhhhh
Q psy17504         23 TCISCGILLTK-GDLFGMRDEMIYCRPHYEILR   54 (196)
Q Consensus        23 ~C~~C~~~L~~-G~~f~~~~~~~~C~~~y~~~~   54 (196)
                      +|..|..+|.. |...+.+.+.++|+.||..+|
T Consensus         1 KCscC~~~LgeiG~s~ytk~~mILCk~DY~rlF   33 (34)
T d1rutx2           1 KCSSCQAQLGDIGTSSYTKSGMILCRNDYIRLF   33 (34)
T ss_dssp             BCTTTCCBHHHHCSEEEEETTEEECHHHHHHHH
T ss_pred             CCcchhcChhhccchheecCCEEEEchhHHHhc
Confidence            47888988844 667788899999999999887

>d1x4ka1 g.39.1.3 (A:35-66) Four and a half LIM domains protein 2, FHL2 {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Four and a half LIM domains protein 2, FHL2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=94.64  E-value=0.0041  Score=32.90  Aligned_cols=30  Identities=27%  Similarity=0.536  Sum_probs=25.2

Q ss_pred             hhhhcceeccCCccccccceeeeccchhhhh
Q psy17504         24 CISCGILLTKGDLFGMRDEMIYCRPHYEILR   54 (196)
Q Consensus        24 C~~C~~~L~~G~~f~~~~~~~~C~~~y~~~~   54 (196)
                      |..|.+++ .-..|..+++..||-.||...|
T Consensus         2 C~~C~qPI-Gtksfipk~~~~yCvpCyE~kf   31 (32)
T d1x4ka1           2 CHRCQQPI-GTKSFIPKDNQNFCVPCYEKQH   31 (32)
T ss_dssp             CSSSCCCC-CSSSEEEETTEEEEHHHHHHHT
T ss_pred             cccccCcc-cccccccCCCCceEeecchhhc
Confidence            78899999 3347888999999999998765

>d1wyha1 g.39.1.3 (A:35-66) Four and a half LIM domains 3, FHL3 {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Four and a half LIM domains 3, FHL3
species: Human (Homo sapiens) [TaxId: 9606]

Probab=94.24  E-value=0.0066  Score=32.06  Aligned_cols=30  Identities=30%  Similarity=0.470  Sum_probs=25.1

Q ss_pred             hhhhcceeccCCccccccceeeeccchhhhh
Q psy17504         24 CISCGILLTKGDLFGMRDEMIYCRPHYEILR   54 (196)
Q Consensus        24 C~~C~~~L~~G~~f~~~~~~~~C~~~y~~~~   54 (196)
                      |..|.+++ .-..|..+++..||-.||+..|
T Consensus         2 C~~C~qPI-GtkSFip~~~~~yCvpCYE~kf   31 (32)
T d1wyha1           2 CSGCEQPL-GSRSFVPDKGAHYCVPCYENKF   31 (32)
T ss_dssp             CTTTCCBT-TTSCEEEETTEEEEHHHHHHHT
T ss_pred             cccccCcc-cccccccCCCcEEEEecccccc
Confidence            78899999 3447888999999999998765

>d2co8a1 g.39.1.3 (A:44-76) Nedd9 interacting protein with calponin homology, NICAL (MICAL1) {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Nedd9 interacting protein with calponin homology, NICAL (MICAL1)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=93.75  E-value=0.008  Score=31.63  Aligned_cols=30  Identities=27%  Similarity=0.473  Sum_probs=24.0

Q ss_pred             hhhhhcceeccCCc-cccccceeeeccchhh
Q psy17504         23 TCISCGILLTKGDL-FGMRDEMIYCRPHYEI   52 (196)
Q Consensus        23 ~C~~C~~~L~~G~~-f~~~~~~~~C~~~y~~   52 (196)
                      .|-+|...|.+|+. +...+|.+||..|+++
T Consensus         1 rC~~CeatL~pG~Y~qhp~dghfyc~~hlpq   31 (33)
T d2co8a1           1 RCHTCEATLWPGGYEQHPGDGHFYCLQHLPQ   31 (33)
T ss_dssp             BCSSSCCBCCTTSEECCTTTCCCEETTTCCC
T ss_pred             CceeeeeEEccCcccCCCCCceEeeeeccCC
Confidence            37788899999984 4667899999998753

>d2dloa1 g.39.1.3 (A:8-42) Thyroid receptor interacting protein 6, TRIP6 {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Thyroid receptor interacting protein 6, TRIP6
species: Human (Homo sapiens) [TaxId: 9606]

Probab=92.63  E-value=0.00073  Score=36.87  Aligned_cols=17  Identities=29%  Similarity=0.661  Sum_probs=15.3

Q ss_pred             HHHHHHHHhHHHhhhhh
Q psy17504          6 SELVMRARDLVFHLHCF   22 (196)
Q Consensus         6 ~~~v~~a~~~~~H~~CF   22 (196)
                      .|.++||.++.||..||
T Consensus        19 ~driLrA~Gk~yHP~CF   35 (35)
T d2dloa1          19 LDRILRAMGKAYHPGCF   35 (35)
T ss_dssp             CSCCEEETTEEECTTTC
T ss_pred             HHHHHHHhCCCCCCCCC
Confidence            46788999999999998

>d1x64a2 g.39.1.3 (A:53-83) PDZ and LIM domain protein 3, PDLIM3 {Mouse (Mus musculus) [TaxId: 10090]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: PDZ and LIM domain protein 3, PDLIM3
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=90.73  E-value=0.024  Score=29.36  Aligned_cols=27  Identities=26%  Similarity=0.667  Sum_probs=20.6

Q ss_pred             hhhhcceeccCCccccccceeeeccchh
Q psy17504         24 CISCGILLTKGDLFGMRDEMIYCRPHYE   51 (196)
Q Consensus        24 C~~C~~~L~~G~~f~~~~~~~~C~~~y~   51 (196)
                      |.-|+..|..-..|. .++.+||+.|..
T Consensus         2 C~dCg~NLKqrG~Ff-v~~~lyCE~HAr   28 (31)
T d1x64a2           2 CADCNLNLKQKGYFF-VEGELYCETHAR   28 (31)
T ss_dssp             CSSSCCCTTTSCCEE-ETTEEECHHHHH
T ss_pred             ccccccChhhcceEE-eccEEeehhhhh
Confidence            788999996554554 588999998854

>d1v6ga2 g.39.1.3 (A:42-81) Actin-binding LIM protein 2, abLIM2 {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Actin-binding LIM protein 2, abLIM2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=90.36  E-value=0.028  Score=30.78  Aligned_cols=30  Identities=20%  Similarity=0.485  Sum_probs=25.6

Q ss_pred             hhhhhhcceeccCCccccccceeeeccchh
Q psy17504         22 FTCISCGILLTKGDLFGMRDEMIYCRPHYE   51 (196)
Q Consensus        22 F~C~~C~~~L~~G~~f~~~~~~~~C~~~y~   51 (196)
                      |.|.+|.+++-.|+.-.+....-+|+.|-+
T Consensus         1 FvC~vCr~pFP~GDRVTFnGKeC~CQ~Cs~   30 (40)
T d1v6ga2           1 FVCAVCRLPFPPGDRVTFNGKECMCQKCSL   30 (40)
T ss_dssp             SSCSSSCCCCCSSSCEEEETTEEEEHHHHS
T ss_pred             CcccccCCCCCCCCeEEEcCceeehhhcCC
Confidence            789999999999998887777889988853

>d1x63a2 g.39.1.3 (A:45-76) Four and a half LIM domains protein 1, FHL-1 {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Four and a half LIM domains protein 1, FHL-1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=89.78  E-value=0.04  Score=28.29  Aligned_cols=31  Identities=26%  Similarity=0.460  Sum_probs=23.5

Q ss_pred             hhhhhcceeccCCccccccceeeeccchhhhh
Q psy17504         23 TCISCGILLTKGDLFGMRDEMIYCRPHYEILR   54 (196)
Q Consensus        23 ~C~~C~~~L~~G~~f~~~~~~~~C~~~y~~~~   54 (196)
                      +|+.|...+..|.. ..+...+||-.|+...|
T Consensus         1 tcs~ckq~igsgsf-fpkg~d~ycvtche~kf   31 (32)
T d1x63a2           1 TCSNCKQVIGTGSF-FPKGEDFYCVTCHETKF   31 (32)
T ss_dssp             CCSSSCCCCTTSCE-EEETTEEEEHHHHHHHT
T ss_pred             Ccchhhhhcccccc-cCCCCcEEEEEeecccc
Confidence            48889998866654 44677899999887654

>d1j2oa2 g.39.1.3 (A:31-63) Rhombotin-2 (Lmo2) {Mouse (Mus musculus) [TaxId: 10090]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Rhombotin-2 (Lmo2)
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=89.06  E-value=0.039  Score=28.77  Aligned_cols=30  Identities=27%  Similarity=0.449  Sum_probs=22.9

Q ss_pred             hhhhhcceecc-CCccccccceeeeccchhh
Q psy17504         23 TCISCGILLTK-GDLFGMRDEMIYCRPHYEI   52 (196)
Q Consensus        23 ~C~~C~~~L~~-G~~f~~~~~~~~C~~~y~~   52 (196)
                      .|..|..+|.. |...+.+.+.++|+.||-.
T Consensus         2 kC~cC~cRLGEVG~tlytk~nliLCkrDYlR   32 (33)
T d1j2oa2           2 SCDLCGCRLGEVGRRLYYKLGRKLCRRDYLR   32 (33)
T ss_dssp             CCSSSCSCCCCSSSCCCCBTTBCCCHHHHHH
T ss_pred             ccccccccccchhhHHHhhcceeeehhhhhc
Confidence            57888888843 4455667899999999964

>d1x3ha1 g.39.1.3 (A:8-42) Leupaxin {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Leupaxin
species: Human (Homo sapiens) [TaxId: 9606]

Probab=88.32  E-value=0.0061  Score=33.31  Aligned_cols=15  Identities=40%  Similarity=0.716  Sum_probs=13.1

Q ss_pred             HHHHHHhHHHhhhhh
Q psy17504          8 LVMRARDLVFHLHCF   22 (196)
Q Consensus         8 ~v~~a~~~~~H~~CF   22 (196)
                      .++.|+++.||..||
T Consensus        21 ~~v~Al~~~wHpeCF   35 (35)
T d1x3ha1          21 NYLSAMDTVWHPECF   35 (35)
T ss_dssp             SCEEETTEEECTTTC
T ss_pred             hheeecCCccCcccC
Confidence            367899999999998

>d1x62a1 g.39.1.3 (A:43-73) PDZ and LIM domain protein 1 Elfin {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: PDZ and LIM domain protein 1 Elfin
species: Human (Homo sapiens) [TaxId: 9606]

Probab=87.96  E-value=0.024  Score=29.46  Aligned_cols=27  Identities=33%  Similarity=0.742  Sum_probs=20.3

Q ss_pred             hhhhcceeccCCccccccceeeeccchh
Q psy17504         24 CISCGILLTKGDLFGMRDEMIYCRPHYE   51 (196)
Q Consensus        24 C~~C~~~L~~G~~f~~~~~~~~C~~~y~   51 (196)
                      |.-|+..|..-..|. .++++||+.|..
T Consensus         2 C~dCg~NLKqrG~Ff-ve~~lyCE~HAr   28 (31)
T d1x62a1           2 CTDCGTNLKQKGHFF-VEDQIYCEKHAR   28 (31)
T ss_dssp             CSSSCCCHHHHCCEE-SSSCEECHHHHH
T ss_pred             ccccccChhhcceEE-eccEEehhhhhh
Confidence            788998885544554 588999998854

>d2dj7a2 g.39.1.3 (A:8-43) Actin-binding LIM protein 3, abLIM-3 {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Actin-binding LIM protein 3, abLIM-3
species: Human (Homo sapiens) [TaxId: 9606]

Probab=86.94  E-value=0.021  Score=30.73  Aligned_cols=11  Identities=45%  Similarity=0.939  Sum_probs=9.9

Q ss_pred             HHhHHHhhhhh
Q psy17504         12 ARDLVFHLHCF   22 (196)
Q Consensus        12 a~~~~~H~~CF   22 (196)
                      |.++.||++||
T Consensus        26 ALdkqWH~~CF   36 (36)
T d2dj7a2          26 ALDKQWHVSCF   36 (36)
T ss_dssp             ETTEEECTTTC
T ss_pred             eeecceeeeeC
Confidence            67889999998

>d2cupa2 g.39.1.3 (A:35-65) Four and a half LIM domains protein 1, FHL-1 {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Four and a half LIM domains protein 1, FHL-1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=85.36  E-value=0.08  Score=27.21  Aligned_cols=27  Identities=26%  Similarity=0.501  Sum_probs=22.9

Q ss_pred             hhhhhcceeccCCccccccceeeeccch
Q psy17504         23 TCISCGILLTKGDLFGMRDEMIYCRPHY   50 (196)
Q Consensus        23 ~C~~C~~~L~~G~~f~~~~~~~~C~~~y   50 (196)
                      +|..|-.+| ..+.|...+++++|..+.
T Consensus         1 RCaKC~hpL-A~E~F~aKd~kI~C~Kc~   27 (31)
T d2cupa2           1 RCAKCLHPL-ANETFVAKDNKILCNKCT   27 (31)
T ss_dssp             CCSSSCCCT-TSSCCEEETTEEECHHHH
T ss_pred             Cchhhcccc-ccCcccccCCeEeecccc
Confidence            478888899 788999999999997764

>d1x68a2 g.39.1.3 (A:37-70) Four and a half LIM domains protein 5, FHL-5 {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Four and a half LIM domains protein 5, FHL-5
species: Human (Homo sapiens) [TaxId: 9606]

Probab=80.30  E-value=0.38  Score=24.85  Aligned_cols=25  Identities=28%  Similarity=0.668  Sum_probs=21.1

Q ss_pred             hhhhcceeccCCccccccceeeeccc
Q psy17504         24 CISCGILLTKGDLFGMRDEMIYCRPH   49 (196)
Q Consensus        24 C~~C~~~L~~G~~f~~~~~~~~C~~~   49 (196)
                      |..|.-.| .|.-|.-....++|+.|
T Consensus         2 cgkcsvsl-vg~gfltq~~~i~c~~c   26 (34)
T d1x68a2           2 CGKCSVSL-VGKGFLTQNKEIFCQKC   26 (34)
T ss_dssp             CTTTCCBC-SSSCEEEETTEEEETTT
T ss_pred             CccceEEE-EeeeeeeccCcEEehhc
Confidence            67788888 78888878889999987